diff --git a/migrations/028_discussions_mr_fk.sql b/migrations/028_discussions_mr_fk.sql
new file mode 100644
index 0000000..9053830
--- /dev/null
+++ b/migrations/028_discussions_mr_fk.sql
@@ -0,0 +1,58 @@
+-- Migration 028: Add FK constraint on discussions.merge_request_id
+-- Schema version: 28
+-- Fixes missing foreign key that causes orphaned discussions when MRs are deleted
+
+-- SQLite doesn't support ALTER TABLE ADD CONSTRAINT, so we must recreate the table.
+
+-- Step 1: Create new table with the FK constraint
+CREATE TABLE discussions_new (
+    id INTEGER PRIMARY KEY,
+    gitlab_discussion_id TEXT NOT NULL,
+    project_id INTEGER NOT NULL REFERENCES projects(id) ON DELETE CASCADE,
+    issue_id INTEGER REFERENCES issues(id) ON DELETE CASCADE,
+    merge_request_id INTEGER REFERENCES merge_requests(id) ON DELETE CASCADE,  -- FK was missing!
+    noteable_type TEXT NOT NULL CHECK (noteable_type IN ('Issue', 'MergeRequest')),
+    individual_note INTEGER NOT NULL DEFAULT 0,
+    first_note_at INTEGER,
+    last_note_at INTEGER,
+    last_seen_at INTEGER NOT NULL,
+    resolvable INTEGER NOT NULL DEFAULT 0,
+    resolved INTEGER NOT NULL DEFAULT 0,
+    raw_payload_id INTEGER REFERENCES raw_payloads(id),  -- Added in migration 004
+    CHECK (
+        (noteable_type = 'Issue' AND issue_id IS NOT NULL AND merge_request_id IS NULL) OR
+        (noteable_type = 'MergeRequest' AND merge_request_id IS NOT NULL AND issue_id IS NULL)
+    )
+);
+
+-- Step 2: Copy data (only rows with valid FK references to avoid constraint violations)
+INSERT INTO discussions_new
+SELECT d.* FROM discussions d
+WHERE (d.merge_request_id IS NULL OR EXISTS (SELECT 1 FROM merge_requests m WHERE m.id = d.merge_request_id));
+
+-- Step 3: Drop old table and rename
+DROP TABLE discussions;
+ALTER TABLE discussions_new RENAME TO discussions;
+
+-- Step 4: Recreate ALL indexes that were on the discussions table
+-- From migration 002 (original table)
+CREATE UNIQUE INDEX uq_discussions_project_discussion_id ON discussions(project_id, gitlab_discussion_id);
+CREATE INDEX idx_discussions_issue ON discussions(issue_id);
+CREATE INDEX idx_discussions_mr ON discussions(merge_request_id);
+CREATE INDEX idx_discussions_last_note ON discussions(last_note_at);
+-- From migration 003 (orphan detection)
+CREATE INDEX idx_discussions_last_seen ON discussions(last_seen_at);
+-- From migration 006 (MR indexes)
+CREATE INDEX idx_discussions_mr_id ON discussions(merge_request_id);
+CREATE INDEX idx_discussions_mr_resolved ON discussions(merge_request_id, resolved, resolvable);
+-- From migration 017 (who command indexes)
+CREATE INDEX idx_discussions_unresolved_recent ON discussions(project_id, last_note_at) WHERE resolvable = 1 AND resolved = 0;
+CREATE INDEX idx_discussions_unresolved_recent_global ON discussions(last_note_at) WHERE resolvable = 1 AND resolved = 0;
+-- From migration 019 (list performance)
+CREATE INDEX idx_discussions_issue_resolved ON discussions(issue_id, resolvable, resolved);
+-- From migration 022 (notes query optimization)
+CREATE INDEX idx_discussions_issue_id ON discussions(issue_id);
+
+-- Record migration
+INSERT INTO schema_version (version, applied_at, description)
+VALUES (28, strftime('%s', 'now') * 1000, 'Add FK constraint on discussions.merge_request_id');
diff --git a/src/core/db.rs b/src/core/db.rs
index c4da226..ce70cfb 100644
--- a/src/core/db.rs
+++ b/src/core/db.rs
@@ -93,6 +93,10 @@ const MIGRATIONS: &[(&str, &str)] = &[
         "027",
         include_str!("../../migrations/027_surgical_sync_runs.sql"),
     ),
+    (
+        "028",
+        include_str!("../../migrations/028_discussions_mr_fk.sql"),
+    ),
 ];
 
 pub fn create_connection(db_path: &Path) -> Result<Connection> {
@@ -130,21 +134,20 @@ pub fn create_connection(db_path: &Path) -> Result<Connection> {
 }
 
 pub fn run_migrations(conn: &Connection) -> Result<()> {
-    let has_version_table: bool = conn
-        .query_row(
-            "SELECT COUNT(*) > 0 FROM sqlite_master WHERE type='table' AND name='schema_version'",
-            [],
-            |row| row.get(0),
-        )
-        .unwrap_or(false);
+    // Note: sqlite_master always exists, so errors here indicate real DB problems
+    // (corruption, locked, etc.) - we must not silently treat them as "fresh DB"
+    let has_version_table: bool = conn.query_row(
+        "SELECT COUNT(*) > 0 FROM sqlite_master WHERE type='table' AND name='schema_version'",
+        [],
+        |row| row.get(0),
+    )?;
 
     let current_version: i32 = if has_version_table {
         conn.query_row(
             "SELECT COALESCE(MAX(version), 0) FROM schema_version",
             [],
             |row| row.get(0),
-        )
-        .unwrap_or(0)
+        )?
     } else {
         0
     };