Thanks for your answer, I checked but it doesn't seem to be the issue.
I made sure that every file is lowercase, and that every "<a></a>" link in my html files are lowercase as well.
What I was saying is that:
- Before the "HTML to ZIP" conversion: every links are lowercase, and points to lowercase files, and every files exists and are lowercase.
- After the "HTML to ZIP" conversion: some duplicate pages with uppercase names are added (e.g.: "AN9.421.xhtml" which is a duplicate to "an9.42.xhtml") and some internal links are modified to point to the duplicated uppercase files instead of the lowercase ones (but only for the 3 files I mentionned in the first post)
Edit: I could modify the ZIP files after the conversion so that they point to the correct lowercase files as a last resort, but I would like to know if there is a way to make everything consistent during the conversion, without having to make modifications after.