'Tis a major worry.
I have the operating system and all the "programmes" on an SSD drive C.
I try to stop the "major churners" from using that for their data. They think they're using drive C, but the PC knows to shift them quietly elsewhere.
My "stuff" is on a conventional hard drive D, and e-mails, iTunes, and other such on another hard drive. They all get backed up on a rota to four different external drives. I think the theory is that the Windows backup could recreate my drive C if anything hosed it, but I bet that's not the case in reality.