Loo-b-loo

Hello I'm having real problems with my WHS2011 system and my Win10 install on my main computer not working well together - so I have decided to format the whs2011 operating drive and install win10 in the hope that my systems will once again get along with each other. My c drive is on its own ssd and my drive pool is a made up of several sata drives in hot swap bays, so I can disconnect them from the system whilst I reinstall, but because there is so much data on there I am worried that (like with WHSv1) if you install a new operating system, the files will not be seen properly by the computer once I reconnect them and I'll end up with lots of bits of files and no complete ones. In doing my research to understand how painful it will be to change the OS, I've read a few posts on here that suggest it should be a really simple job to deactivate the licence on the current whs2011 OS, install the new os and stablebit and 'bobs your uncle' all will be fine and all my worry will be for nothing. Is it really this easy? Any help or advice (in plain English please) for an amateur home server enthusiast would be much appreciated. Louise