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AO3 has its own epub download feature, so have an epub of an AO3 fanfic is not a guarantee that it's from FFF.
FanFicFare(FFF) can output mobi files as a legacy feature, but it's kind of terrible and I recommend epub output and calibre convert for all users.
Renaming a mobi to epub will definitely not work--the formats are completely different.
FFF anthologies can only be created as epubs.
If you still have an epub that won't open for you (and it's SFW), please post it for me to see.
Have you do an new downloads using FFF? Do they work correctly?
My initial thoughts are possible disk errors or full disk issues.
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