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If you are referring to additional files written inside the epub by a reader (such as the calibre reader), yes it does.
We talk about 'updating the epub', but in reality, FFDL harvests what it recognizes as valid chapters (and images) from the old epub and uses them as input to generate a completely new epub. Anything it doesn't explicitly copy over is lost. It's very similar to the issue with keeping custom covers.
In the beta version posted above, I trained FFDL to recognize and keep covers, but that's it so far.
If we can confirm that your problem is caused by a file inside the epub being discarded (and identify the file), I can make FFDL carry it forward.
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