diff --git a/cli/src/internal/maintenance/upgradePrestart.cjs b/cli/src/internal/maintenance/upgradePrestart.cjs
index effbafc0..d865792a 100644
--- a/cli/src/internal/maintenance/upgradePrestart.cjs
+++ b/cli/src/internal/maintenance/upgradePrestart.cjs
@@ -211,15 +211,25 @@ async function prestartBackend(
 }
 
 async function cleanSqliteBuildArtifacts(directory) {
-  const names = await fs.readdir(directory).catch((error) => {
+  const entries = await fs.readdir(directory, { withFileTypes: true }).catch((error) => {
     if (error.code !== 'ENOENT') throw error;
     return [];
   });
-  // node-pre-gyp's runtime copy lives in lib/binding. Its build directories
-  // retain compiler objects and an absolute node_gyp_bins/python3 symlink.
-  for (const name of names)
-    if (name === 'build' || /^build-tmp-napi-v\d+$/.test(name))
-      await fs.rm(path.join(directory, name), { recursive: true, force: true });
+  if (!entries.length) return;
+  const pkg = JSON.parse(await fs.readFile(path.join(directory, 'package.json'), 'utf8'));
+  const runtimePath = path.posix.normalize(pkg.binary?.module_path || '.');
+  const copiedRuntime = runtimePath.startsWith('lib/binding/');
+  // Our legacy fork copies its runtime to lib/binding. Other sqlite3 versions
+  // load build/Release directly: retain that addon and remove only the compiler
+  // helper directory. Never traverse a build-directory symlink while cleaning.
+  for (const entry of entries) {
+    if (entry.name !== 'build' && !/^build-tmp-napi-v\d+$/.test(entry.name)) continue;
+    const build = path.join(directory, entry.name);
+    await fs.rm(
+      copiedRuntime || entry.isSymbolicLink() ? build : path.join(build, 'node_gyp_bins'),
+      { recursive: true, force: true },
+    );
+  }
 }
 
 async function repairDependencies(source, { target, signal, env }) {
diff --git a/test/back/migration-sqlite-armv6.test.cjs b/test/back/migration-sqlite-armv6.test.cjs
index a82f1aeb..3d033c80 100644
--- a/test/back/migration-sqlite-armv6.test.cjs
+++ b/test/back/migration-sqlite-armv6.test.cjs
@@ -37,7 +37,7 @@ async function fixture(t) {
     await fs.mkdir(path.join(root, name), { recursive: true });
   await fs.writeFile(root + '/package.json', JSON.stringify({ qinglongMigrationBridge: { format: 1 }, dependencies: { sqlite3: 'legacy' } }));
   await fs.writeFile(root + '/pnpm-lock.yaml', 'fixed legacy lock');
-  await fs.writeFile(root + '/node_modules/sqlite3/package.json', '{}');
+  await fs.writeFile(root + '/node_modules/sqlite3/package.json', JSON.stringify({ binary: { module_path: './lib/binding/napi-v{napi_build_version}-{platform}-{arch}' } }));
   await fs.writeFile(root + '/runtime/include/node/node_version.h', '#define NODE_MAJOR_VERSION 24\n#define NODE_MINOR_VERSION 18\n#define NODE_PATCH_VERSION 1\n');
   return { root, runtime: { execPath: root + '/runtime/bin/node', versions: { node: '24.18.1' }, env: { PATH: '/qa/bin', NODE_OPTIONS: '--require=untrusted', CFLAGS: '-march=armv7' } } };
 }
diff --git a/test/back/upgrade-prestart.test.cjs b/test/back/upgrade-prestart.test.cjs
index 5d6bb6db..d242f887 100644
--- a/test/back/upgrade-prestart.test.cjs
+++ b/test/back/upgrade-prestart.test.cjs
@@ -8,6 +8,7 @@ const {
   dependencyFailure,
   probeLimits,
   repairDependencies,
+  cleanSqliteBuildArtifacts,
 } = require('../../cli/src/internal/maintenance/upgradePrestart.cjs');
 
 for (const exitCode of [0, 1])
@@ -291,7 +292,7 @@ test('successful legacy repair publishes only portable runtime files from a pnpm
     const pkg = 'node_modules/.pnpm/@whyour+sqlite3@1.1.2/node_modules/@whyour/sqlite3';
     if (process.argv[2] === 'install') {
       fs.mkdirSync(pkg + '/lib/binding/napi-v6-linux-arm', {recursive:true});
-      fs.writeFileSync(pkg + '/package.json', '{}');
+      fs.writeFileSync(pkg + '/package.json', JSON.stringify({binary:{module_path:'./lib/binding/napi-v{napi_build_version}-{platform}-{arch}'}}));
       fs.symlinkSync('.pnpm/@whyour+sqlite3@1.1.2/node_modules/@whyour/sqlite3', 'node_modules/sqlite3');
     } else if (process.argv[2] === 'rebuild') {
       fs.writeFileSync(pkg + '/lib/binding/napi-v6-linux-arm/node_sqlite3.node', 'compiled addon');
@@ -331,6 +332,26 @@ test('successful legacy repair publishes only portable runtime files from a pnpm
   await inventory({ source });
 });
 
+test('cleanup retains sqlite3 runtimes loaded from build/Release and never follows a build symlink', async (t) => {
+  const root = await fs.mkdtemp(path.join(os.tmpdir(), 'ql-sqlite-release-'));
+  t.after(() => fs.rm(root, { recursive: true, force: true }));
+  const sqlite = path.join(root, 'sqlite3'), outside = path.join(root, 'outside');
+  await fs.mkdir(path.join(sqlite, 'build/Release'), { recursive: true });
+  await fs.mkdir(path.join(sqlite, 'build/node_gyp_bins'));
+  await fs.mkdir(path.join(outside, 'node_gyp_bins'), { recursive: true });
+  await fs.writeFile(path.join(outside, 'node_gyp_bins/keep'), 'untouched');
+  await fs.writeFile(path.join(sqlite, 'package.json'), JSON.stringify({ name: 'sqlite3', binary: { napi_versions: [3, 6] } }));
+  await fs.writeFile(path.join(sqlite, 'build/Release/node_sqlite3.node'), 'runtime addon');
+  await fs.symlink('/usr/bin/python3', path.join(sqlite, 'build/node_gyp_bins/python3'));
+  await fs.symlink(outside, path.join(sqlite, 'build-tmp-napi-v3'));
+  await cleanSqliteBuildArtifacts(sqlite);
+  assert.equal(await fs.readFile(path.join(sqlite, 'build/Release/node_sqlite3.node'), 'utf8'), 'runtime addon');
+  await assert.rejects(fs.access(path.join(sqlite, 'build/node_gyp_bins')), { code: 'ENOENT' });
+  await assert.rejects(fs.lstat(path.join(sqlite, 'build-tmp-napi-v3')), { code: 'ENOENT' });
+  assert.equal(await fs.readFile(path.join(outside, 'node_gyp_bins/keep'), 'utf8'), 'untouched');
+  await require('../../cli/src/internal/maintenance/platformBundle.cjs').inventory({ source: sqlite });
+});
+
 test('repair classification excludes application, platform, config, database, OOM and timeouts', () => {
   for (const error of [
     { code: 'MODULE_NOT_FOUND', message: "Cannot find module './api/missing'" },