that doesn't seem right though because i have updated the apple firmware previously and it hasn't erased the bootloader.
Why not try it instead of arguing with me?
so basically do i just run the ipodpatcher.exe again and then everything is back to normal or do i have to put the .rockbox crap back on there. does it completely restore my system?
Unless you actually "restored" the iPod through iTunes, which erases everything, simply upgrading the iPod firmware should not impact the .rockbox folder so you should not have to reinstall the Rockbox build. Besides, you already indicated that you installed a Rockbox build after you did the update, so this is really a moot point.
So, yes, just run ipodpatcher again, as I indicated in my last post.