Repairing Vista using the Startup Repair option ( http://www.bleepingcomputer.com/tutorials/repair-windows-with-windows-startup-repair/
) won't harm your data.
Neither will a full repair of Vista ( http://vistasupport.mvps.org/repair_a_vist...e_vista_dvd.htm
But, as with any major work on the OS - backing up your stuff is advised prior to attempting the repair. If you don't have the space to back them up - what are you going to do if your hard drive actually does die? I'd advise getting a USB hard drive to back your data up on. You could also back it up to the secondary hard drive (if it's a separate hard drive and not just another partition on the physical hard drive).
There's several ways to do this outside of Windows, so if you need advice on this, let us know.
As for removing the second Vista installation - boot into your Vista installation, go to Disk Management and format the other hard drive. If the computer still thinks that second installation is there after rebooting, you can run the Startup Repair to fix that.
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