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I've moved programs before from the C drive partition to another partition, and although one worked with no problems, the other (software for digital camcorder) did have some problems. I even uninstalled and reinstalled onto the newer partition, but the program would not work unless the folder that contained the works-in-progress stayed on C. The main program folders were fine being on the other drive. I just could not convince the program to let me keep the pendings folder (where the camera uploads the media for it to be converted to mpg or avi) on any other drive than C.
So...for your problem, its a flip of the coin on whether it will work well by moving things.
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