if you have set it as the master then when you reboot your computer it would look for that hd and it will not find it since you remove the jumper and you will have a disk boot error. why do you have to remove it?
The primary usage for a jumper is to assign 'master' and 'slave' when you have two drives: If you have two hard drives, then you might cause real problems One hard drive = I've never had trouble, but don't blame me if it gets messed up What's the issue? Are you having trouble booting up?
All newer hard drives have a printed diagram showing the jumper settings. If you know the model, the info can usually be found at the web site of the maker. There are usually 6 pins. The options are master, slave, cable select and just parked. Just parked and no jumper are exactly the same except you store the jumper on the hard drive. SATA drives do not use jumpers since there is only one drive per cable.
Removal of jumper will not cause any damage to your HDs but will probably fix the problem .I have experienced it so many times.