diff --git a/extensions/ql-vscode/src/databases.ts b/extensions/ql-vscode/src/databases.ts
index 50b9e4223..2a9d5a1aa 100644
--- a/extensions/ql-vscode/src/databases.ts
+++ b/extensions/ql-vscode/src/databases.ts
@@ -684,7 +684,9 @@ export class DatabaseManager extends DisposableObject {
         this._onDidChangeDatabaseItem.fire(event);
       });
 
-    await this.addDatabaseItem(progress, token, item);
+    // Avoid persisting the database state after adding since that should happen only after
+    // all databases have been added.
+    await this.addDatabaseItem(progress, token, item, false);
     return item;
   }
 
@@ -724,6 +726,7 @@ export class DatabaseManager extends DisposableObject {
               void this.logger.log(`Error loading database ${database.uri}: ${e}.`);
             }
           }
+          await this.updatePersistedDatabaseList();
         } catch (e) {
           // database list had an unexpected type - nothing to be done?
           void showAndLogErrorMessage(`Database list loading failed: ${getErrorMessage(e)}`);
@@ -784,10 +787,14 @@ export class DatabaseManager extends DisposableObject {
   private async addDatabaseItem(
     progress: ProgressCallback,
     token: vscode.CancellationToken,
-    item: DatabaseItem
+    item: DatabaseItem,
+    updatePersistedState = true
   ) {
     this._databaseItems.push(item);
-    await this.updatePersistedDatabaseList();
+
+    if (updatePersistedState) {
+      await this.updatePersistedDatabaseList();
+    }
 
     // Add this database item to the allow-list
     // Database items reconstituted from persisted state
diff --git a/extensions/ql-vscode/src/legacy-query-server/run-queries.ts b/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
index 009aba070..4f95933ee 100644
--- a/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
+++ b/extensions/ql-vscode/src/legacy-query-server/run-queries.ts
@@ -54,7 +54,7 @@ export class QueryInProgress {
   }
 
   get compiledQueryPath() {
-    return path.join(this.querySaveDir, 'compiledQuery.qlo');
+    return this.queryEvalInfo.compileQueryPath;
   }
 
 
diff --git a/extensions/ql-vscode/src/run-queries-shared.ts b/extensions/ql-vscode/src/run-queries-shared.ts
index 11d96e129..3c158be9c 100644
--- a/extensions/ql-vscode/src/run-queries-shared.ts
+++ b/extensions/ql-vscode/src/run-queries-shared.ts
@@ -192,7 +192,7 @@ export class QueryEvaluationInfo {
     if (await this.hasDil()) {
       return this.dilPath;
     }
-    const compiledQuery = path.join(this.querySaveDir, 'compiledQuery.qlo');
+    const compiledQuery = this.compileQueryPath;
     if (!(await fs.pathExists(compiledQuery))) {
       if (await cliServer.cliConstraints.supportsNewQueryServer()) {
         // This could be from the new query server