Didn't there use to be some issue with mobi->mobi conversions? I can't recall the details, someone will. Personally I always keep ePub, make any changes I want to that, and then convert to mobi. I don't read on a device using ePub since I only read on my Kindle, but ePub is a far more easily editable format to make sure only the changes you want get applied.
The other question I would ask is what are you trying to do with save to disk and creating a new library? If you just want to move your library, that is easily done in other ways. If you have some other reason for a new library, just use calibre to create library and then use right-click Copy to Library to make sure you keep every single bit of your metadata.
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