If you patch a game, usually the patch maker has used junk bytes in the rom to make the patch. Because trimming removes those junk bytes, applying a patch afterwards will always fail, unless the patch maker has taken this into account. By modifying the rom, the header and other data will also be altered, thus if you trim afterwards, the trimming utility doesn't recognize the rom properly and it will result in a broken rom. Patch makers will usually trim the rom to the right size after making a patch, so you don't need to. If you really want to be certain that the game is trimmed, even though you've patched, you can open the rom up in a hex editor and remove all 00 or FF bytes at the end (do this at own risk though)