This is an ongoing issue for us.
The scripts aren't being deleted anymore. I think 16.0.3 solved that issue, but we are still losing our custom menu set and value lists.
The only thing I've been able to do is restore from backup and manually search for modified data to import from the damaged copy.
FileMaker server 16.0.3 running on MacOS 10.12.6
All clients have updated to 16.0.3. Startup script doesn't even allow users with version less than 16.0.3 to connect.