I could see the database being corrupted if the bad files caused a crash and reboot while the database was being written, but in the cases where the files are not processed, I don't think so. The firmware seems to process all the files and the database updates happen at the end in one go.
As to the crash, PeterT's suggestion is good. Look for some stack logs and supply a file that causes the problem. Kobo are the one who need to see it, but I'm curious to look as well. Ideally supplying a link to a freely available manga would be the best. But, putting one somewhere and sending me the link in a PM will also work.
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