Thanks for letting me know, I don't use OSX often, so I wasn't aware of this problem.
The patch only includes files that need to be changed, the rest of them should be preserved, as you found out.
On windows, when you copy a folder into another folder, it doesn't delete anything in the folder, it just replaces any duplicate files - i didn't know that wasn't the case on OSX. Is there any other way around this on OSX? If not, I might have to change the patch to make it easier to install - sorry for the trouble!