Hello,
i've a similar problem.
i've digitalized a book of mines (it's the first time!

) and edited it, deleting all the hyphens that in the paper book divided words at the end of lines, than i've saved it as rtf and imported to my Calibre library.
then i've converted it (with Calibre) to fb2 and all the hyphens have magically reappeared! the same happens if i convert the .rtf to .prc but not if I convert it to .epub
which is the problem? do you have any advice? i'd like to have it in fb2 or prc/mobi...
another issue i could not solve is about the footnotes. they are correctly viewed in the original rtf document but they are lost in the conversion. how could i manage this problem?
thank you in advance
best regards