Wierd, cause I did this and the floppy went all "clank-clank" and sounded nasty. I figured it probably would be ok until later (I left it connected for a week or so this way, multiple reboots, etc....). Now that floppy drive is dead and had to be replaced. In my experiences, yes, it can screw it up.
I'd connected it backwards before and it continued working, but this time, it didn't.