I created a simple test file with Sigil that contains Latin, Hebrew and Arabic file names with combining diacritics. It also contains one file name without combining diacritics. Sigil had no problems with any of them.
However, EPUBCheck reported that it couldn't find the second
résumé.xhtml file, which contained the letter e followed by a combining acute diacritic.
Code:
Col: -1: ERROR(RSC-001): File "OEBPS/Text/re%CC%81sume%CC%81.xhtml" could not be found.
But since the path seems to be properly URL encoded this might actually be an EPUBCheck bug.
Maybe this is the problem that the user is referring to.
IMHO, using combining Unicode characters instead of precomposed characters isn't a good idea anyway, because many fonts don't contain glyphs for them.