I have a larger hard drive that is empty than the 80gb HDD that I am using. I would like to remove WindowsXP from the smaller 80 gb HDD but not all the programs/.exe files from the 80gb HDD. Can I just add/remove Windows from the 80gb HDD reinstall WindowsXP on the empty drive and then connect them to the Motherboard?
No.
You will still need to reinstall all of the programs after you reinstall windows other wise the registry of the new install wont know about the programs left on the other drive.
The best thing you could do is to backup (just in case) any documents, songs, movies or anything that you dont want to lose.
Take out the old drive and put in the new one and install windows.
Then put in the old one and use it as a data drive.
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