Welcome to the forum @ilyai
I don’t use Windows Server 2016 (anybody out there using it who has specific additional comment?), but Duplicati probably just sees at as Windows. You might need to make sure .NET Framework is up to date.
There’s never a guarantee that you didn’t back something up the wrong way if you have more than simple closed files. If you have files that are in use by some application, data might not be on drive yet to back up.
Databases are especially likely to give specific procedures, but even desktop applications can have them.
Volume Shadow Copy Service can help with this (by working with VSS-aware applications), if you set up snapshot-policy in Duplicati (which requires putting Administrator privilege in effect, which can be difficult).
There’s never a guarantee that a recovery will work, and whether or not you tune is pretty much up to you. None of this is Windows Server 2016 specific though. For best reliability, you should use several backups.
For large backups, one good tuning for performance is to increase blocksize. This helps database actions. Choosing sizes in Duplicati talks about some other possible tunings, but lots of people likely don’t bother…