it shouldn't harm them at all. i've done it before - when i desperately needed to do a defrag, and the files (SHNs/FLACs) verified OK after defragmenting the drive.

but, if you feel iffy about defragging with "important data" on your drive, maybe you should clear off the stuff (if possible) first. of course, that would make defragmenting your HD faster.

as an aside note, if you're a PC user (i don't know if you're on a Mac/PC) i suggest staying away from Windows built-in defragmenter, and using something like Diskeeper. it's much better for your HD, and MUCH faster than Windows built-in utility.

aside #2, something that works well for me is this: partitioning my HD, so i have the O/S on "C" drive, and have "D" and "E" drives for data only. i save downloaded torrents on the 'data' drives, and burn them off as quickly as possible. when i've saved everything i want/need to (onto CDR/DVDR), i simply format the D/E partitions (using Partition Magic). it's even faster than defragmenting, and from what i've read, better for the drive as well.