The utilities plugin uses "VACUUM" on the database to compress it. I would expect any SQLite database manager to do the same thing. From memory, this works by copying the data to an empty database. I would expect some integrity problems to be OK with this. An index error would not cause a problem. A page marked as in use, but with nothing pointing to it would probably be OK. The error you had looks to be one of these.
I doubt the compress would fix a problem if a pointer to a page was broken. That is what is usually reported when there is an error during the sync with calibre. In these cases, even if the compress worked, there would probably be some data loss.
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