Restoring replaces what is on the server right now. That is the point, and it is also the danger: if you restore the wrong snapshot, the thing you overwrote is gone unless you saved it first.
It sounds absurd to back up something you are trying to get rid of, but it is what makes a restore reversible. If the snapshot you pick turns out to be older than you thought, you can still get back to where you were.
What to do
- Stop the server
Restoring under a running server produces a mix of old and new files, which is worse than either.
- Pick the snapshot by date, not by position
«The last one» is not always the right one. If corruption started on Tuesday, Monday's backup is the one you want, not this morning's.
- Restore, then start and look before playing
Join and check a few builds you know the state of. It is much cheaper to notice you restored too far back before ten people build on top of it.
If the problem is a corrupted world but your configuration is fine, unpacking only the world folders from the archive keeps your plugin setup intact instead of rolling everything back.
The server starts, the world loads, and the builds you checked are in the state you expected for that date.