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For my purposes, the last time I factory reset a Kobo, I transferred the 4200 books that were on it back in one batch and they were imported without issue. I then restored the reading status using Kobo Utilities and all went well.
One item though is that I have editing all my ebooks for years and they pass epubcheck without real errors before being moved from my Intake library to my Main library in calibre.
Quite a few fanfics that I downloaded were a total mess with code that is not supported by ePub being used so epubcheck spewed pages of error messages. Not to mention committing the sin of using absolute sizes. Yeah, the result may have looked good on the author's 10" high-res Android tablet but looked like crap on a 6" screen ereader.
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