diff --git a/plugin/scripts/context-generator.cjs b/plugin/scripts/context-generator.cjs
index 06697dc7..81549f1a 100644
--- a/plugin/scripts/context-generator.cjs
+++ b/plugin/scripts/context-generator.cjs
@@ -69,7 +69,7 @@ ${o.stack}`:` ${o.message}`:this.getLevel()===0&&typeof o=="object"?_=`
       CREATE INDEX IF NOT EXISTS idx_session_summaries_sdk_session ON session_summaries(memory_session_id);
       CREATE INDEX IF NOT EXISTS idx_session_summaries_project ON session_summaries(project);
       CREATE INDEX IF NOT EXISTS idx_session_summaries_created ON session_summaries(created_at_epoch DESC);
-    `),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(4,new Date().toISOString())}ensureWorkerPortColumn(){this.db.query("PRAGMA table_info(sdk_sessions)").all().some(s=>s.name==="worker_port")||(this.db.run("ALTER TABLE sdk_sessions ADD COLUMN worker_port INTEGER"),m.debug("DB","Added worker_port column to sdk_sessions table")),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(5,new Date().toISOString())}ensurePromptTrackingColumns(){this.db.query("PRAGMA table_info(sdk_sessions)").all().some(a=>a.name==="prompt_counter")||(this.db.run("ALTER TABLE sdk_sessions ADD COLUMN prompt_counter INTEGER DEFAULT 0"),m.debug("DB","Added prompt_counter column to sdk_sessions table")),this.db.query("PRAGMA table_info(observations)").all().some(a=>a.name==="prompt_number")||(this.db.run("ALTER TABLE observations ADD COLUMN prompt_number INTEGER"),m.debug("DB","Added prompt_number column to observations table")),this.db.query("PRAGMA table_info(session_summaries)").all().some(a=>a.name==="prompt_number")||(this.db.run("ALTER TABLE session_summaries ADD COLUMN prompt_number INTEGER"),m.debug("DB","Added prompt_number column to session_summaries table")),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(6,new Date().toISOString())}removeSessionSummariesUniqueConstraint(){if(!this.db.query("PRAGMA index_list(session_summaries)").all().some(s=>s.unique===1)){this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(7,new Date().toISOString());return}m.debug("DB","Removing UNIQUE constraint from session_summaries.memory_session_id"),this.db.run("BEGIN TRANSACTION"),this.db.run("DROP TABLE IF EXISTS session_summaries_new"),this.db.run(`
+    `),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(4,new Date().toISOString())}ensureWorkerPortColumn(){this.db.query("PRAGMA table_info(sdk_sessions)").all().some(s=>s.name==="worker_port")||(this.db.run("ALTER TABLE sdk_sessions ADD COLUMN worker_port INTEGER"),m.debug("DB","Added worker_port column to sdk_sessions table")),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(5,new Date().toISOString())}ensurePromptTrackingColumns(){this.db.query("PRAGMA table_info(sdk_sessions)").all().some(a=>a.name==="prompt_counter")||(this.db.run("ALTER TABLE sdk_sessions ADD COLUMN prompt_counter INTEGER DEFAULT 0"),m.debug("DB","Added prompt_counter column to sdk_sessions table")),this.db.query("PRAGMA table_info(observations)").all().some(a=>a.name==="prompt_number")||(this.db.run("ALTER TABLE observations ADD COLUMN prompt_number INTEGER"),m.debug("DB","Added prompt_number column to observations table")),this.db.query("PRAGMA table_info(session_summaries)").all().some(a=>a.name==="prompt_number")||(this.db.run("ALTER TABLE session_summaries ADD COLUMN prompt_number INTEGER"),m.debug("DB","Added prompt_number column to session_summaries table")),this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(6,new Date().toISOString())}removeSessionSummariesUniqueConstraint(){if(!this.db.query("PRAGMA index_list(session_summaries)").all().some(s=>s.unique===1&&s.origin!=="pk")){this.db.prepare("INSERT OR IGNORE INTO schema_versions (version, applied_at) VALUES (?, ?)").run(7,new Date().toISOString());return}m.debug("DB","Removing UNIQUE constraint from session_summaries.memory_session_id"),this.db.run("BEGIN TRANSACTION"),this.db.run("DROP TABLE IF EXISTS session_summaries_new"),this.db.run(`
       CREATE TABLE session_summaries_new (
         id INTEGER PRIMARY KEY AUTOINCREMENT,
         memory_session_id TEXT NOT NULL,
diff --git a/src/services/sqlite/SessionStore.ts b/src/services/sqlite/SessionStore.ts
index d7d853a7..748b3026 100644
--- a/src/services/sqlite/SessionStore.ts
+++ b/src/services/sqlite/SessionStore.ts
@@ -217,7 +217,7 @@ export class SessionStore {
   private removeSessionSummariesUniqueConstraint(): void {
     // Check actual constraint state — don't rely on version tracking alone (issue #979)
     const summariesIndexes = this.db.query('PRAGMA index_list(session_summaries)').all() as IndexInfo[];
-    const hasUniqueConstraint = summariesIndexes.some(idx => idx.unique === 1);
+    const hasUniqueConstraint = summariesIndexes.some(idx => idx.unique === 1 && idx.origin !== 'pk');
 
     if (!hasUniqueConstraint) {
       // Already migrated (no constraint exists)
diff --git a/src/services/sqlite/migrations/runner.ts b/src/services/sqlite/migrations/runner.ts
index 2e404735..a3d31a29 100644
--- a/src/services/sqlite/migrations/runner.ts
+++ b/src/services/sqlite/migrations/runner.ts
@@ -189,7 +189,7 @@ export class MigrationRunner {
   private removeSessionSummariesUniqueConstraint(): void {
     // Check actual constraint state — don't rely on version tracking alone (issue #979)
     const summariesIndexes = this.db.query('PRAGMA index_list(session_summaries)').all() as IndexInfo[];
-    const hasUniqueConstraint = summariesIndexes.some(idx => idx.unique === 1);
+    const hasUniqueConstraint = summariesIndexes.some(idx => idx.unique === 1 && idx.origin !== 'pk');
 
     if (!hasUniqueConstraint) {
       // Already migrated (no constraint exists)