diff --git a/server/src/__tests__/document-annotations-service.test.ts b/server/src/__tests__/document-annotations-service.test.ts
index ff616b65..054e57db 100644
--- a/server/src/__tests__/document-annotations-service.test.ts
+++ b/server/src/__tests__/document-annotations-service.test.ts
@@ -230,4 +230,44 @@ describeEmbeddedPostgres("documentAnnotationService", () => {
     expect(updatedThread?.status).toBe("resolved");
     expect(updatedThread?.resolvedByUserId).toBe("board-user");
   });
+
+  it("rejects annotation comments linked to already-deleted issue comments", async () => {
+    const { companyId, issueId, document } = await createIssueWithDocument();
+    const [issueComment] = await db
+      .insert(issueComments)
+      .values({
+        companyId,
+        issueId,
+        authorType: "user",
+        authorUserId: "board-user",
+        body: "",
+        deletedAt: new Date("2026-06-05T03:00:00.000Z"),
+        deletedByType: "user",
+        deletedByUserId: "board-user",
+      })
+      .returning();
+
+    await expect(
+      annotations.createThread(
+        issueId,
+        "plan",
+        {
+          baseRevisionId: document.latestRevisionId!,
+          baseRevisionNumber: document.latestRevisionNumber,
+          selector: {
+            quote: { exact: "selected text", prefix: "Alpha ", suffix: " omega" },
+            position: { normalizedStart: 6, normalizedEnd: 19, markdownStart: 6, markdownEnd: 19 },
+          },
+          body: "Do not link this annotation to a deleted comment",
+          issueCommentId: issueComment.id,
+        },
+        { actorType: "user", actorId: "board-user", userId: "board-user" },
+      ),
+    ).rejects.toMatchObject({
+      status: 422,
+      message: "Linked issue comment must belong to this issue",
+    });
+
+    await expect(db.select().from(documentAnnotationComments)).resolves.toHaveLength(0);
+  });
 });
diff --git a/server/src/services/document-annotations.ts b/server/src/services/document-annotations.ts
index f7aa70e3..3de9cf02 100644
--- a/server/src/services/document-annotations.ts
+++ b/server/src/services/document-annotations.ts
@@ -1,4 +1,4 @@
-import { and, asc, desc, eq, inArray, sql } from "drizzle-orm";
+import { and, asc, desc, eq, inArray, isNull, sql } from "drizzle-orm";
 import type { Db } from "@paperclipai/db";
 import {
   documentAnnotationAnchorSnapshots,
@@ -155,7 +155,7 @@ export function documentAnnotationService(db: Db) {
         issueId: issueComments.issueId,
       })
       .from(issueComments)
-      .where(eq(issueComments.id, commentId))
+      .where(and(eq(issueComments.id, commentId), isNull(issueComments.deletedAt)))
       .then((rows: Array<{ id: string; companyId: string; issueId: string }>) => rows[0] ?? null);
     if (!comment || comment.issueId !== issueId) {
       throw unprocessable("Linked issue comment must belong to this issue");
diff --git a/ui/src/components/IssueChatThread.test.tsx b/ui/src/components/IssueChatThread.test.tsx
index c4af6461..5afbe981 100644
--- a/ui/src/components/IssueChatThread.test.tsx
+++ b/ui/src/components/IssueChatThread.test.tsx
@@ -1270,7 +1270,6 @@ describe("IssueChatThread", () => {
   it("confirms and invokes delete only for the current user's normal comments", async () => {
     const root = createRoot(container);
     const onDeleteComment = vi.fn(async () => {});
-    const confirmSpy = vi.spyOn(window, "confirm").mockReturnValue(true);
 
     act(() => {
       root.render(
@@ -1324,10 +1323,17 @@ describe("IssueChatThread", () => {
       deleteButtons[0]?.dispatchEvent(new MouseEvent("click", { bubbles: true }));
     });
 
-    expect(confirmSpy).toHaveBeenCalled();
+    expect(document.body.textContent).toContain("Delete comment?");
+    const confirmButton = Array.from(document.body.querySelectorAll("button"))
+      .find((button) => button.textContent === "Delete comment");
+    expect(confirmButton).toBeTruthy();
+
+    await act(async () => {
+      confirmButton?.dispatchEvent(new MouseEvent("click", { bubbles: true }));
+    });
+
     expect(onDeleteComment).toHaveBeenCalledWith("comment-owned");
 
-    confirmSpy.mockRestore();
     act(() => {
       root.unmount();
     });
diff --git a/ui/src/components/IssueChatThread.tsx b/ui/src/components/IssueChatThread.tsx
index ef5576bc..7470ae4f 100644
--- a/ui/src/components/IssueChatThread.tsx
+++ b/ui/src/components/IssueChatThread.tsx
@@ -1290,6 +1290,7 @@ function IssueChatUserMessage({
   const deleted = Boolean(custom.deletedAt);
   const queueTargetRunId = typeof custom.queueTargetRunId === "string" ? custom.queueTargetRunId : null;
   const [copied, setCopied] = useState(false);
+  const [deleteDialogOpen, setDeleteDialogOpen] = useState(false);
   const {
     isCurrentUser,
     authorName: resolvedAuthorName,
@@ -1309,8 +1310,11 @@ function IssueChatUserMessage({
   const canDeleteComment = Boolean(onDeleteComment && isCurrentUser && !queued && !pending && !deleted);
   const handleDeleteComment = () => {
     if (!canDeleteComment) return;
-    const confirmed = window.confirm("Delete this comment? This will replace it with a deleted-comment marker.");
-    if (!confirmed) return;
+    setDeleteDialogOpen(true);
+  };
+  const confirmDeleteComment = () => {
+    if (!canDeleteComment) return;
+    setDeleteDialogOpen(false);
     void onDeleteComment?.(commentId);
   };
   const messageBody = (
@@ -1432,21 +1436,41 @@ function IssueChatUserMessage({
   );
 
   return (
-    <div id={anchorId}>
-      <div className={cn("group flex items-start gap-2.5", isCurrentUser && "justify-end")}>
-        {isCurrentUser ? (
-          <>
-            {messageBody}
-            {authorAvatar}
-          </>
-        ) : (
-          <>
-            {authorAvatar}
-            {messageBody}
-          </>
-        )}
+    <>
+      <div id={anchorId}>
+        <div className={cn("group flex items-start gap-2.5", isCurrentUser && "justify-end")}>
+          {isCurrentUser ? (
+            <>
+              {messageBody}
+              {authorAvatar}
+            </>
+          ) : (
+            <>
+              {authorAvatar}
+              {messageBody}
+            </>
+          )}
+        </div>
       </div>
-    </div>
+      <Dialog open={deleteDialogOpen} onOpenChange={setDeleteDialogOpen}>
+        <DialogContent>
+          <DialogHeader>
+            <DialogTitle>Delete comment?</DialogTitle>
+            <DialogDescription>
+              This will replace the comment with a deleted-comment marker.
+            </DialogDescription>
+          </DialogHeader>
+          <DialogFooter>
+            <Button variant="outline" onClick={() => setDeleteDialogOpen(false)}>
+              Cancel
+            </Button>
+            <Button variant="destructive" onClick={confirmDeleteComment}>
+              Delete comment
+            </Button>
+          </DialogFooter>
+        </DialogContent>
+      </Dialog>
+    </>
   );
 }
 
diff --git a/ui/src/pages/IssueDetail.tsx b/ui/src/pages/IssueDetail.tsx
index 65fce726..7e41c4ca 100644
--- a/ui/src/pages/IssueDetail.tsx
+++ b/ui/src/pages/IssueDetail.tsx
@@ -2461,20 +2461,6 @@ export function IssueDetail() {
   const cancelQueuedComment = useMutation({
     mutationFn: async ({ commentId }: { commentId: string }) => issuesApi.cancelComment(issueId!, commentId),
     onSuccess: (comment) => {
-      if (comment.deletedAt) {
-        upsertCommentInCache(comment);
-        clearCommentHashIfCurrent(comment.id);
-        invalidateIssueDetail();
-        invalidateIssueThreadLazily();
-        invalidateIssueCollections();
-        invalidateIssueDocumentAnnotationState();
-        pushToast({
-          title: "Comment deleted",
-          body: "The comment was replaced with a deleted marker.",
-          tone: "success",
-        });
-        return;
-      }
       setLocallyQueuedCommentRunIds((current) => {
         if (!current.has(comment.id)) return current;
         const next = new Map(current);