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Make a Copy First!
It has been stated before, but bears repeating:
You should not be changing the database in your actual Calibre library. You should be making a copy first and modifying that.
Just as the DB schema change broke Calibre Sync, changing your library DB might prevent Calibre itself from using your library in a future version.
My personal script uses rsync to quickly update the copy of my library, then changes the DB file before sync'ing it to my device.
I also want to reiterate: the issue isn't the change to Calibre, it's the fact Calibre Sync is not being maintained now.
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