This is a known issue with the DS File app. It does not properly integrate into the iOS Files subsystem. This has been reported to Synology but a fix does not seem imminent. Typically the database becomes stale/old and Strongbox is unable to update it. Unfortunately this appears to be a poor integration by the Synology DS File app.
The only reliable way to connect to a database hosted on a Synology server is via SFTP or WebDAV. This works well in practice. You can find out how to turn on WebDAV on your Synology NAS here:
https://strongboxsafe.com/updates/syncing-with-synology-nas/
There is absolutely nothing that can be done from the Strongbox side here as Strongbox just requests read/write operations via iOS and iOS communicates with the DS File app to coordinate this. It is entirely up to the DS File app to honour those requests which it seems to perform poorly if at all.