Consideration
When restoring a backup (.fsconfig) taken from FME Server 2020 or 2021 to FME Flow 2022 or later, any user-created workspaces stored in the Tools repository will not be restored. No errors or warnings are produced during the restore — the data is silently omitted.
Why This Happens
The Tools repository was a default repository bundled with FME Server installations up to and including 2021.x. It originally housed workspaces used by Automations for Filter and Log actions, which were replaced by dedicated native actions in FME Server 2020.0. As a result, the Tools repository was removed from the FME Flow installer beginning in 2022.0.
Because the Tools repository no longer exists on a fresh FME Flow 2022+ installation, the Backup & Restore process has no target repository to restore its contents into, and skips it without logging a warning.
How to Resolve It
If you still have access to the source server:
Before taking your backup, move or republish any workspaces from the Tools repository to another repository. They will then be included correctly when restoring to FME Flow.
If you no longer have access to the source server:
The .fsconfig backup file is a ZIP archive. Rename it with a .zip extension and open it. Locate any workspaces inside the files folder, then republish them to your FME Flow instance. You may need to create a new repository first to publish them into.