When applying a patch file to a directory this will normally replace some files in that directory. In order to allow end users to restore old versions of the software, those files are preserved by moving them to a backup directory. This backup directory defaults to a subdirectory named "Backup" but this can be changed using the GenPatch option "-backup=AnotherDir" which makes the patch file use this as the backup directory.
Note that we recommend that you specify this differently for each version, since any file already present in the backup directory will be overwritten when applying the patch. Applying the same patch several times will be no problem since that will not change any file and therefore won't impose the need to replace anything. Please also note that embedded files may also replace existing ones and these will be moved to the backup directory, too.
The so-called "deleted" files are actually only moved to the backup directory and not really physically deleted. To clean up and prevent waste of disk space you might tell you users or create a batch file to delete the backup directory after applying patches.