A correct Apocalypse install will only have only one file named "fileA" in a folder, using whichever case the OS/mounting tool decides to use:
filea, fileA, FileA, FILEA, FiLeA, or anything in between.
If there will be two or more files having the same name (albeit with different case) in the same folder, this is user error, and there should be no attempt by the game to find the "right" file. The current approach is right.
Is it worth checksuming the original files to guard against bad installs/patched files & such?