Should work fine, but only if you do a good job.
Keep the longest part, I read somewhere that a to long cable is bad (18+inches) and a too short cable is bad as well (believe it was something like 4 Inches, not sure though).
I've got an old (40 wire) IDE cable that has only one connector and that works fine, and the only difference between a 40 and a 80 wire cable is that the 80 wire cable has 40 Xtra wires connected to ground/earth.
I suggest you cut the cable with some scissors (that should leave a clean cut) and as close to the connector as possible, but before you do that you might wanna try it with a VERY sharp exacto knife (practice on the part you wanna get rid of), and see if you get a nice clean cut from that.
Nice clean cut=NO copper wires sticking out (you don't wanna short circuit your rig and/or HD).
Good luck (don't think you'll need that though)