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You need to rebuild the index(es) if you delete a row.
Collections can certainly be easily recreated from Calibre to the Kobo*.
@Davidfor would know about the other things.
I personally only care about annotations FROM the Kobo to PC via Kobo Utilities, which are saved in plain text files. You could note current % read for any open books. I did that for a couple of books the time I loaded an earlier backup of the database when it broke (rare). Obviously a backed up database has nothing about what you did since. The backup was renamed to the standard name on the kobo after the broken database was deleted. My backup names is <name of kobo, there are 3 here><date><version if more than one that day>
[* That and series is why 2 of the 3 main reasons I use a kobo not a Kindle]
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