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I have been using the Bitbucket Server backup client for a few years. Backups used to take an hour. We needed to expand and move data to a NetApp mount in a different location. The first backup after the move was still running when business began so I stopped it.
I let it run twice on the weekend thinking it would catch up after the first time but the second time took 10 hours. Should I delete all the backup files to get it to "reset"?
This sounds like you've moved your backups to a much slower file system, and the best place to look would be getting a faster file system.
I'd like to confirm what you mean by "Bitbucket Server backup client", but if it is what I guess it is, then no, deleting old backups won't have any effect, the backups are not incremental or staged, they're a simple one-off dump of everything.
It's weird because the old daily logs look like they're only scanning repositories that changed that day. Then after the move and update to the new home directory, the next log shows it is scanning all repositories. The log after that scans all repositories again.
But now that we moved to NetApp, we're using hourly snapshots. We tested restoring to a snapshot and database backup. With that, I was able to convince my manager that these nightly backups with the client are not needed anymore.