Any programs installed on a drive connected by way of the usb bus are too vulnerable. With XP or Vista downloading the replacement software from the support sie and reformatting the factory Fat32 partition to NTFS would also be recommended. XP and Vista alike will still recognise the drive as a logical drive even if the software gets knocked out.
But programs installed and run by way of usb will have problems! If it was simply a custom install to a second internal drive like many see with desktops you wouldn't run into the usb snare where suddenly programs won't run. In addition to that the primary purpose for the external drives are addon storage not for softwares or even OSing them.
You can try all you want but expect problems as far as reliability when going to run any programs you custom install there. The programs you count on the most should still be seen on the internal drive while extras you can experiment with at your own risk in that sense. Programs like Adobe and MS will certainly look at the C drive as home simply by default and may not even allow for custom installation to a second partition or drive.
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