No, even if you installed Vista on a second drive, most apps installed under XP would NOT work under Vista.
XP x64 was always going to be a dead end path, and you should have taken note of this before you went ahead and installed it. XP x64 was never really intended for widescale distribution. It was mostly a dry run for Vista x64, and also to make a few big name clients happy who do a lot of things that would have benefited from a 64-bit OS.
I would like to upgrade XP ProX64 to Ultimate X64, unfortunately everything I have read says the upgrade has to be clean. This would entail re-installing over a hundred programs. Of course if someone knows of a way to avoid this everything would be simple solution. I have thought of installing a full backup including system after Ultimate X64, but afraid this will not work. I know I can install and boot the two OSs but first can I do this with an upgrade Ultimate X64 on the second drive while keeping XP intact and second if this can be done will the original programs work?

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