5
When you copy a file into a directory on your local hard drive, does it delete all other files? Nope, it doesn't. No files will be deleted.
There are about 100 files in the patch and those 100 files will be overwritten, if they exist.
If you have installed e.g. a gallery module, no files in that module will be overwritten as it has no files in the patch.
If you do not have modules such as contact, xoopspoll and xoopsheadline uploaded to the server, just don't upload those files from the patch.