@edeniz -
Re: Anthologies: Those files are there as part of EpubMerge's 'UnMerge' feature, which is how FFF makes Anthologies that it can update. There is currently no way in FFF to remove them. If you can prove that the extra files cause a problem, I will look into making it optional. One option now is to not use the Anthology feature in FFF and instead download individual stories and then manually use EpubMerge with 'Keep UnMerge Data' turned off.
Re: Stripping tags: Removing whitespace only containing tags that aren't 'p','td','th' is functioning as designed. If you want, you adjust the value of
keep_empty_tags to add more tags to keep when empty.
I'm going to need to see an example of actual text being removed accidentally before I can troubleshoot that. Plus, you have
replace_br_with_p set true, which introduces a bunch of heuristic tag editing. I would guess that you found an example of poor input HTML being handled badly.