diff --git a/CHANGELOG.md b/CHANGELOG.md
index 69c839d736..df57698372 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -37,6 +37,11 @@ and this project adheres to
 
 ### Fixed
 
+- Sandbox merge no longer deletes a workflow that was added to the project after
+  the sandbox was branched. Workflows present in the project but not the sandbox
+  now default to kept (removal is opt-in) and are labelled clearly in the merge
+  screen. [#4919](https://github.com/OpenFn/lightning/issues/4919)
+
 ## [2.16.8] - 2026-07-01
 
 ## [2.16.8-pre] - 2026-06-18
diff --git a/lib/lightning_web/live/sandbox_live/components.ex b/lib/lightning_web/live/sandbox_live/components.ex
index 69412da638..b851eff111 100644
--- a/lib/lightning_web/live/sandbox_live/components.ex
+++ b/lib/lightning_web/live/sandbox_live/components.ex
@@ -370,32 +370,49 @@ defmodule LightningWeb.SandboxLive.Components do
                 </span>
                 <span
                   :if={wf.is_changed && !wf.is_new && !wf.is_deleted}
+                  id={"merge-wf-changed-#{wf.id}"}
                   class="flex items-center gap-1 text-xs font-medium text-green-700"
-                  title="This workflow has been modified in the sandbox"
+                  phx-hook="Tooltip"
+                  aria-label="This workflow has been modified in the sandbox"
                 >
                   Changed
                 </span>
                 <span
                   :if={wf.is_diverged}
+                  id={"merge-wf-diverged-#{wf.id}"}
                   class="flex items-center gap-1 text-xs font-medium text-amber-700"
-                  title="This workflow was modified in the target project - this change will be lost"
+                  phx-hook="Tooltip"
+                  aria-label="This workflow was modified in the target project - this change will be lost"
                 >
                   <.icon name="hero-exclamation-triangle-mini" class="h-3.5 w-3.5" />
                   Diverged
                 </span>
                 <span
                   :if={wf.is_new}
+                  id={"merge-wf-new-#{wf.id}"}
                   class="flex items-center gap-1 text-xs font-medium text-blue-700"
-                  title="This workflow doesn't exist in the target — it will be created"
+                  phx-hook="Tooltip"
+                  aria-label="This workflow doesn't exist in the target — it will be created"
                 >
                   New
                 </span>
                 <span
-                  :if={wf.is_deleted}
-                  class="flex items-center gap-1 text-xs font-medium text-red-700"
-                  title="This workflow was deleted in the sandbox — selecting it will delete it from the target"
+                  :if={wf.is_deleted && wf.added_after_fork}
+                  id={"merge-wf-added-#{wf.id}"}
+                  class="flex items-center gap-1 text-xs font-medium text-gray-500"
+                  phx-hook="Tooltip"
+                  aria-label="Added to the project after this sandbox was created. Check to delete it from the project."
                 >
-                  Deleted in sandbox
+                  Added to the project after this sandbox was created
+                </span>
+                <span
+                  :if={wf.is_deleted && !wf.added_after_fork}
+                  id={"merge-wf-existed-#{wf.id}"}
+                  class="flex items-center gap-1 text-xs font-medium text-gray-500"
+                  phx-hook="Tooltip"
+                  aria-label="In the project but not in this sandbox. Check to delete it from the project."
+                >
+                  In the project but not in this sandbox
                 </span>
               </li>
             </ul>
diff --git a/lib/lightning_web/live/sandbox_live/index.ex b/lib/lightning_web/live/sandbox_live/index.ex
index 242d3f88a1..1ec704eaeb 100644
--- a/lib/lightning_web/live/sandbox_live/index.ex
+++ b/lib/lightning_web/live/sandbox_live/index.ex
@@ -14,7 +14,15 @@ defmodule LightningWeb.SandboxLive.Index do
   require Logger
 
   defmodule MergeWorkflow do
-    defstruct [:id, :name, :is_changed, :is_diverged, :is_new, :is_deleted]
+    defstruct [
+      :id,
+      :name,
+      :is_changed,
+      :is_diverged,
+      :is_new,
+      :is_deleted,
+      added_after_fork: false
+    ]
   end
 
   on_mount {LightningWeb.Hooks, :project_scope}
@@ -890,6 +898,7 @@ defmodule LightningWeb.SandboxLive.Index do
         }
       end)
 
+    # Target-only workflows default to unchecked so a merge never silently deletes them.
     deleted_entries =
       target_workflows
       |> Enum.reject(fn wf -> MapSet.member?(source_workflow_names, wf.name) end)
@@ -897,10 +906,11 @@ defmodule LightningWeb.SandboxLive.Index do
         %MergeWorkflow{
           id: wf.id,
           name: wf.name,
-          is_changed: true,
+          is_changed: false,
           is_diverged: false,
           is_new: false,
-          is_deleted: true
+          is_deleted: true,
+          added_after_fork: workflow_added_after_fork?(wf, source)
         }
       end)
 
@@ -908,31 +918,34 @@ defmodule LightningWeb.SandboxLive.Index do
     |> Enum.sort_by(fn wf -> wf.name end)
   end
 
-  defp resolve_selected_workflow_ids(assigns) do
-    all_ids = MapSet.new(assigns.merge_source_workflows, fn wf -> wf.id end)
+  defp workflow_added_after_fork?(%{inserted_at: %DateTime{} = wf_inserted}, %{
+         inserted_at: %DateTime{} = fork_time
+       }) do
+    DateTime.compare(wf_inserted, fork_time) == :gt
+  end
 
-    if MapSet.equal?(assigns.merge_selected_workflow_ids, all_ids) do
-      {nil, nil}
-    else
-      deleted_ids =
-        assigns.merge_source_workflows
-        |> Enum.filter(fn wf -> wf.is_deleted end)
-        |> MapSet.new(fn wf -> wf.id end)
+  defp workflow_added_after_fork?(_workflow, _source), do: false
 
-      selected = assigns.merge_selected_workflow_ids
+  # Always pass an explicit selection so unchecked target-only workflows are kept, not deleted.
+  defp resolve_selected_workflow_ids(assigns) do
+    deleted_ids =
+      assigns.merge_source_workflows
+      |> Enum.filter(fn wf -> wf.is_deleted end)
+      |> MapSet.new(fn wf -> wf.id end)
 
-      selected_source_ids =
-        selected
-        |> Enum.reject(&MapSet.member?(deleted_ids, &1))
-        |> Enum.to_list()
+    selected = assigns.merge_selected_workflow_ids
 
-      selected_deleted_ids =
-        selected
-        |> Enum.filter(&MapSet.member?(deleted_ids, &1))
-        |> Enum.to_list()
+    selected_source_ids =
+      selected
+      |> Enum.reject(&MapSet.member?(deleted_ids, &1))
+      |> Enum.to_list()
 
-      {selected_source_ids, selected_deleted_ids}
-    end
+    selected_deleted_ids =
+      selected
+      |> Enum.filter(&MapSet.member?(deleted_ids, &1))
+      |> Enum.to_list()
+
+    {selected_source_ids, selected_deleted_ids}
   end
 
   defp preload_merge_projects(source, nil),
@@ -991,17 +1004,11 @@ defmodule LightningWeb.SandboxLive.Index do
        ) do
     maybe_commit_to_github(target, "pre-merge commit")
 
-    opts =
-      if selected_workflow_ids do
-        %{
-          selected_workflow_ids: selected_workflow_ids,
-          deleted_target_workflow_ids: deleted_target_workflow_ids
-        }
-      else
-        %{}
-      end
-
-    opts = Map.put(opts, :selected_credential_ids, selected_credential_ids)
+    opts = %{
+      selected_workflow_ids: selected_workflow_ids,
+      deleted_target_workflow_ids: deleted_target_workflow_ids,
+      selected_credential_ids: selected_credential_ids
+    }
 
     case Sandboxes.merge(source, target, actor, opts) do
       {:ok, _updated_target} = success ->
diff --git a/test/lightning_web/live/sandbox_live/index_test.exs b/test/lightning_web/live/sandbox_live/index_test.exs
index c927d80b6b..eefb711154 100644
--- a/test/lightning_web/live/sandbox_live/index_test.exs
+++ b/test/lightning_web/live/sandbox_live/index_test.exs
@@ -3579,16 +3579,22 @@ defmodule LightningWeb.SandboxLive.IndexTest do
       assert MapSet.member?(assigns.merge_selected_workflow_ids, changed_data.id)
     end
 
-    test "target-only workflows appear in list with is_deleted flag and badge",
+    test "target-only workflows appear in list unchecked by default",
          %{
            conn: conn,
            parent: parent,
            sandbox: sandbox
          } do
-      # Parent has "Alpha" and "Gamma" — sandbox only has "Alpha"
-      # so "Gamma" was deleted in the sandbox
+      # Gamma existed before the fork, so it is in the project but not the sandbox.
       _parent_alpha = insert(:workflow, project: parent, name: "Alpha")
-      _parent_gamma = insert(:workflow, project: parent, name: "Gamma")
+
+      _parent_gamma =
+        insert(:workflow,
+          project: parent,
+          name: "Gamma",
+          inserted_at: DateTime.add(sandbox.inserted_at, -3600, :second)
+        )
+
       _sandbox_alpha = insert(:workflow, project: sandbox, name: "Alpha")
 
       {:ok, view, _} = live(conn, ~p"/projects/#{parent.id}/sandboxes")
@@ -3603,16 +3609,107 @@ defmodule LightningWeb.SandboxLive.IndexTest do
       gamma_data =
         Enum.find(assigns.merge_source_workflows, &(&1.name == "Gamma"))
 
-      assert gamma_data
-      assert gamma_data.is_deleted
-      refute gamma_data.is_new
-      refute gamma_data.is_diverged
+      assert %{
+               is_deleted: true,
+               is_new: false,
+               is_diverged: false,
+               is_changed: false,
+               added_after_fork: false
+             } = gamma_data
 
-      # The gamma workflow's ID in the list is the target (parent) workflow ID
-      assert MapSet.member?(assigns.merge_selected_workflow_ids, gamma_data.id)
+      refute MapSet.member?(assigns.merge_selected_workflow_ids, gamma_data.id)
 
-      # Badge shown in HTML
-      assert html =~ "Deleted in sandbox"
+      assert html =~ "In the project but not in this sandbox"
+    end
+
+    test "target-only workflow added after the fork is labelled and kept",
+         %{conn: conn, parent: parent, sandbox: sandbox} do
+      _parent_alpha = insert(:workflow, project: parent, name: "Alpha")
+
+      _parent_added =
+        insert(:workflow,
+          project: parent,
+          name: "Added Later",
+          inserted_at: DateTime.add(sandbox.inserted_at, 3600, :second)
+        )
+
+      _sandbox_alpha = insert(:workflow, project: sandbox, name: "Alpha")
+
+      {:ok, view, _} = live(conn, ~p"/projects/#{parent.id}/sandboxes")
+
+      html =
+        view
+        |> element("#branch-rewire-sandbox-#{sandbox.id} button")
+        |> render_click()
+
+      assigns = :sys.get_state(view.pid).socket.assigns
+
+      added_data =
+        Enum.find(assigns.merge_source_workflows, &(&1.name == "Added Later"))
+
+      assert %{is_deleted: true, is_changed: false, added_after_fork: true} =
+               added_data
+
+      refute MapSet.member?(assigns.merge_selected_workflow_ids, added_data.id)
+
+      assert html =~ "Added to the project after this sandbox was created"
+      refute html =~ "In the project but not in this sandbox"
+    end
+
+    test "explicitly checking a target-only workflow deletes it on merge",
+         %{conn: conn, parent: parent, sandbox: sandbox} do
+      parent_alpha = insert(:workflow, project: parent, name: "Alpha")
+
+      parent_gamma =
+        insert(:workflow,
+          project: parent,
+          name: "Gamma",
+          inserted_at: DateTime.add(sandbox.inserted_at, -3600, :second)
+        )
+
+      _sandbox_alpha = insert(:workflow, project: sandbox, name: "Alpha")
+
+      {:ok, view, _} = live(conn, ~p"/projects/#{parent.id}/sandboxes")
+
+      view
+      |> element("#branch-rewire-sandbox-#{sandbox.id} button")
+      |> render_click()
+
+      render_click(view, "toggle-workflow", %{"id" => parent_gamma.id})
+
+      render_click(view, "confirm-merge", %{
+        "merge" => %{"target_id" => parent.id}
+      })
+
+      assert Lightning.Repo.reload(parent_gamma).deleted_at
+      refute Lightning.Repo.reload(parent_alpha).deleted_at
+    end
+
+    test "target-only workflow is kept when left unchecked on merge",
+         %{conn: conn, parent: parent, sandbox: sandbox} do
+      parent_alpha = insert(:workflow, project: parent, name: "Alpha")
+
+      parent_added =
+        insert(:workflow,
+          project: parent,
+          name: "Added Later",
+          inserted_at: DateTime.add(sandbox.inserted_at, 3600, :second)
+        )
+
+      _sandbox_alpha = insert(:workflow, project: sandbox, name: "Alpha")
+
+      {:ok, view, _} = live(conn, ~p"/projects/#{parent.id}/sandboxes")
+
+      view
+      |> element("#branch-rewire-sandbox-#{sandbox.id} button")
+      |> render_click()
+
+      render_click(view, "confirm-merge", %{
+        "merge" => %{"target_id" => parent.id}
+      })
+
+      refute Lightning.Repo.reload(parent_added).deleted_at
+      refute Lightning.Repo.reload(parent_alpha).deleted_at
     end
 
     test "workflow selection UI shows per-row status badges", %{
@@ -4142,7 +4239,8 @@ defmodule LightningWeb.SandboxLive.IndexTest do
             apiSecretName: api_secret_name(parent),
             branch: repo_connection.branch,
             pathToConfig: path_to_config(repo_connection),
-            commitMessage: "Merged sandbox #{sandbox.name}"
+            commitMessage: "Merged sandbox #{sandbox.name}",
+            snapshots: "#{snapshot.id}"
           }
         }
       )
@@ -4209,7 +4307,8 @@ defmodule LightningWeb.SandboxLive.IndexTest do
             apiSecretName: api_secret_name(parent),
             branch: repo_connection.branch,
             pathToConfig: path_to_config(repo_connection),
-            commitMessage: "Merged sandbox #{sandbox.name}"
+            commitMessage: "Merged sandbox #{sandbox.name}",
+            snapshots: "#{snapshot.id}"
           }
         }
       )