Sorry to hear your having issues with your data!
Welcome to sevenforums!
I am assuming that you are talking USB external drives... Have you tried unplugging, rebooting and then plugging back in?
Perhaps the SP1 update overwrote a proprietary hard drive manufacturers sw... what brand and model drives are these? Im sure your data is still on these drives, the SP1 upgrade wouldnt do anything to your tunes!
Western Digital, and others, external drives frequently use their own software, so you may need to check with your drives manufacturer!