Reinstall Windows

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Bit of advice needed here. I have a SSD for Windows and a HDD for programs, Documents and everything else. I am waiting to reinstall Windows 10 so it's fresh but unsure how to go about this and not sure what would happen to the programs on my HDD. (Never done it with more than one SSD/HDD in my system).

I know how to install Windows and i'll be doing this by unplugging the HDD and installing to the SSD. For my programs, would I just reinstall them over the existing files on the HDD or am I best formatting that too?
 
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Just delete the programs folder (if it's in the same partition as your documents etc) and start it afresh, the new install will not recognise it as programs at all. For Steam on the other hand you can back up the steamapps folder and then copy it over to the new Steam install so it saves you from redownloading all your games.
 
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