diff --git a/extensions/ql-vscode/src/databases-ui.ts b/extensions/ql-vscode/src/databases-ui.ts
index 50d5c14fdc3..e8b9ffd8a31 100644
--- a/extensions/ql-vscode/src/databases-ui.ts
+++ b/extensions/ql-vscode/src/databases-ui.ts
@@ -378,21 +378,28 @@ export class DatabaseUI extends DisposableObject {
 
   handleRemoveOrphanedDatabases = async (): Promise<void> => {
     logger.log('Removing orphaned databases from workspace storage.');
-    let dbDirs =
-      // read directory
-      (await fs.readdir(this.storagePath, { withFileTypes: true }))
-        // remove non-directories
-        .filter(dirent => dirent.isDirectory())
-        // get the full path
-        .map(dirent => path.join(this.storagePath, dirent.name))
-        // remove databases still in workspace
-        .filter(dbDir => {
-          const dbUri = Uri.file(dbDir);
-          return this.databaseManager.databaseItems.every(item => item.databaseUri.fsPath !== dbUri.fsPath);
-        });
-
-    // remove non-databases
-    dbDirs = await asyncFilter(dbDirs, isLikelyDatabaseRoot);
+    let dbDirs = undefined;
+
+    try {
+      dbDirs =
+        // read directory
+        (await fs.readdir(this.storagePath, { withFileTypes: true }))
+          // remove non-directories
+          .filter(dirent => dirent.isDirectory())
+          // get the full path
+          .map(dirent => path.join(this.storagePath, dirent.name))
+          // remove databases still in workspace
+          .filter(dbDir => {
+            const dbUri = Uri.file(dbDir);
+            return this.databaseManager.databaseItems.every(item => item.databaseUri.fsPath !== dbUri.fsPath);
+          });
+
+      // remove non-databases
+      dbDirs = await asyncFilter(dbDirs, isLikelyDatabaseRoot);
+    } catch (e) {
+      logger.log(`Not able to find the storage path '${e.message}'. Ignoring request to remove orphaned database directories.`);
+      return;
+    }
 
     if (!dbDirs.length) {
       logger.log('No orphaned databases found.');
diff --git a/extensions/ql-vscode/src/discovery.ts b/extensions/ql-vscode/src/discovery.ts
index bdad6b22aca..cc89e2fe969 100644
--- a/extensions/ql-vscode/src/discovery.ts
+++ b/extensions/ql-vscode/src/discovery.ts
@@ -1,5 +1,5 @@
 import { DisposableObject } from './vscode-utils/disposable-object';
-import { showAndLogErrorMessage } from './helpers';
+import { logger } from './logging';
 
 /**
  * Base class for "discovery" operations, which scan the file system to find specific kinds of
@@ -62,7 +62,7 @@ export abstract class Discovery<T> extends DisposableObject {
     });
 
     discoveryPromise.catch(err => {
-      showAndLogErrorMessage(`${this.name} failed. Reason: ${err.message}`);
+      logger.log(`${this.name} failed. Reason: ${err.message}`);
     });
 
     discoveryPromise.finally(() => {
diff --git a/extensions/ql-vscode/src/helpers.ts b/extensions/ql-vscode/src/helpers.ts
index cb05510568c..ecfea422a4f 100644
--- a/extensions/ql-vscode/src/helpers.ts
+++ b/extensions/ql-vscode/src/helpers.ts
@@ -123,15 +123,16 @@ export function commandRunner(
     try {
       return await task(...args);
     } catch (e) {
+      const errorMessage = `${e.message || e} (${commandId})`;
       if (e instanceof UserCancellationException) {
         // User has cancelled this action manually
         if (e.silent) {
-          logger.log(e.message);
+          logger.log(errorMessage);
         } else {
-          showAndLogWarningMessage(e.message);
+          showAndLogWarningMessage(errorMessage);
         }
       } else {
-        showAndLogErrorMessage(e.message || e);
+        showAndLogErrorMessage(errorMessage);
       }
       return undefined;
     }
@@ -161,15 +162,16 @@ export function commandRunnerWithProgress<R>(
     try {
       return await withProgress(progressOptionsWithDefaults, task, ...args);
     } catch (e) {
+      const errorMessage = `${e.message || e} (${commandId})`;
       if (e instanceof UserCancellationException) {
         // User has cancelled this action manually
         if (e.silent) {
-          logger.log(e.message);
+          logger.log(errorMessage);
         } else {
-          showAndLogWarningMessage(e.message);
+          showAndLogWarningMessage(errorMessage);
         }
       } else {
-        showAndLogErrorMessage(e.message || e);
+        showAndLogErrorMessage(errorMessage);
       }
       return undefined;
     }
diff --git a/extensions/ql-vscode/src/qltest-discovery.ts b/extensions/ql-vscode/src/qltest-discovery.ts
index 50bb3ee863b..0cda0be3d80 100644
--- a/extensions/ql-vscode/src/qltest-discovery.ts
+++ b/extensions/ql-vscode/src/qltest-discovery.ts
@@ -3,6 +3,7 @@ import { Discovery } from './discovery';
 import { EventEmitter, Event, Uri, RelativePattern, WorkspaceFolder, env } from 'vscode';
 import { MultiFileSystemWatcher } from './vscode-utils/multi-file-system-watcher';
 import { CodeQLCliServer } from './cli';
+import * as fs from 'fs-extra';
 
 /**
  * A node in the tree of tests. This will be either a `QLTestDirectory` or a `QLTestFile`.
@@ -180,19 +181,21 @@ export class QLTestDiscovery extends Discovery<QLTestDiscoveryResults> {
   private async discoverTests(): Promise<QLTestDirectory> {
     const fullPath = this.workspaceFolder.uri.fsPath;
     const name = this.workspaceFolder.name;
-    const resolvedTests = (await this.cliServer.resolveTests(fullPath))
-      .filter((testPath) => !QLTestDiscovery.ignoreTestPath(testPath));
-
     const rootDirectory = new QLTestDirectory(fullPath, name);
-    for (const testPath of resolvedTests) {
-      const relativePath = path.normalize(path.relative(fullPath, testPath));
-      const dirName = path.dirname(relativePath);
-      const parentDirectory = rootDirectory.createDirectory(dirName);
-      parentDirectory.addChild(new QLTestFile(testPath, path.basename(testPath)));
-    }
 
-    rootDirectory.finish();
+    // Don't try discovery on workspace folders that don't exist on the filesystem
+    if ((await fs.pathExists(fullPath))) {
+      const resolvedTests = (await this.cliServer.resolveTests(fullPath))
+        .filter((testPath) => !QLTestDiscovery.ignoreTestPath(testPath));
+      for (const testPath of resolvedTests) {
+        const relativePath = path.normalize(path.relative(fullPath, testPath));
+        const dirName = path.dirname(relativePath);
+        const parentDirectory = rootDirectory.createDirectory(dirName);
+        parentDirectory.addChild(new QLTestFile(testPath, path.basename(testPath)));
+      }
 
+      rootDirectory.finish();
+    }
     return rootDirectory;
   }