Found x remote files that are not recorded in local storage, please run repair

That’s my thought, although I still warn people to avoid collisions, i.e. restores elsewhere during backup.
Best case is it will just see some extra data that it doesn’t see source file use of (that info is in the dlist).
Worst case is something will be more confused by the partial backup. If source system dies, there’s no choice but to pick up the incomplete backup, but if there’s an option, don’t tempt fate. Feel free to test it, because anybody who can find a repeatable failure potentially paves the way to a problem being solved,
or at least a better understanding of the limits of the systems so that forum users can be better advised.

is a current topic talking about what’s safe, less safe, and don’t-do-it, e.g. don’t point two backups to one folder and run them – this will throw things way off. Good testing (including rare cases) can be beneficial.

Testing is one thing, but Duplicati is not a file sync program. Above topic on testing talks about (and gives references for) some different ways to do restores. Database should match the destination that it tracks, and this is easy to foul up when two databases (one per Duplicati installation) are configured to one folder.

Temporary databases (e.g. Direct restore from backup files or Restore from configuration) avoid having an out-of-sync database by building a partial temporary database (slowly?) when they’re run.

If “restore from conf file” means you checked Restore from configuration option (and description of temp db sounds like it was) I’m not sure what it thought was extra. In a small test, I threw an extra dblock file into the destination and it didn’t mind, but possibly there’s a timing thing if it arrives at the wrong time.

You can either see if it does that when things are settled (no backup running) or see if you can get names from About → Show log → Live → Warning. I think it will talk about “Extra unknown file” and name names which can then be looked up to see, for example if they are recently uploaded files from a running backup.

“recorded in local storage” refers to the local database storage, and any message about missing or extra remote files refers to destination files relative to the database record. They aren’t source or restore-target.