Hi there.
Generally I don't use the same name and/or change any file's casing along the way.
That being said, I indeed didn't know about the case sensitivity in Unix-like systems, so naturally I never was too careful about file name casing, beyond my general inclination to keep things somewhat clean.
Could you tell me what files the error was about? Cause, when looking at the collection of files from last update, I don't see any that I have changed the casing of.
Assuming I'm not missing anything, there might be a different reason for said error - so, in the spirit of covering multiple bases at once: Did you use the update-only patch or the full update? And if it was the latter, did you unzip it into a new location or did you overwrite your previous installation of CH?