I don't know how to get Windows to see the drives as new and start over.
Perhaps if it's possible to move all the data from one to the other, formating the blank one (NTFS) you could get Windows to treat it the same as it did previously and see it as a new drive.
If that works you would then repeat the process in the other direction.
Do you have a restore point that is before you ran System Restore in the first place, maybe doing that with the drives disconnected would help.
I'm afraid that going to last good know configuration will just take you to the set up the last time the computer booted.
I'm grasping at straws here but my external drives don't show in Device Manager when they are turned off but maybe turning them on and the telling device manager to disable or uninstall them then rebooting the computer and letting them be discovered again would reset them.
I suppose it wouldn't hurt to try, going to the run box and typing Scf /scannow is worth a shot too.
As a last resort you could try doing a repair install of Window 7, this seems kind of like over kill, but I don't have any other ideas.
It shouldn't take more then a half hour.
http://www.sevenforums.com/tutorials/3413-repair-install.html
Mike