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i thought that if you separate the drives, then formating will only affect either the OS or the programs but not both.
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Correct, but what SK means is most programs are 'linked' to a specific Installation, much like Windows is 'linked' to a specific MoBo. If you swap MoBo's, you will most likely have to reinstall Windows; if you reinstall Windows, you will most likely have to reinstall individual programs.
Take my setup, for example. My Windows HDD has the following partitions: Windows OS, Windows Software, and my personal partition. In my case, separating the OS from the installed software was purely an OCD/organizational preference, not to spare me from reinstalling programs after an OS format/reinstall.