Originally Posted by Jellby
Does that happen when you zip only the modified file into the original ePUB? Valid ePUB files are required to have the "mimetype" file zipped first and uncompressed. If you update only the modified files, the "mimetype" should remain unchanged and therefore the ePUB should remain valid. If the zip program does not behave in this way, it's probably not a bug, but it's weird. If, on the other hand, you are zipping again the whole contents of the original ePUB, don't do that, and update only the modified *.opf file instead.
Yeah I used stuffit archive manager to do this. I actually tried to create an archive from an unzipped folder but it didn't work. Ill try to use the aforementioned program an ill see how it works.