Dual Boot Problems

[Geofilms]

So I recently upgraded my build. I previously used a harddisk but I didn't want to transfer GB upon GBs of old junk onto my new NVME so I installed a fresh windows onto NVME (Samsung 980 pro with updated firmware). My plan was to use my NVME as my main boot drive and wipe my old hard drive and have that as additional storage. However I have exams soon and I have a lot of programs on my harddrive so I didn't want to wipe my hard disk just yet and was planning on booting my NVME for normal usage of my PC and when I wanted to study I would boot from my hard drive. This seems to be causing some minor issues however. 

Issues:
1 day I wanted to play dota (I was booted into my NVME) and noticed my dota (which I installed to my hard drive cause I don't need it to open fast) was no longer on my PC I can still find dota files on my hard drive so I assume there must be some sort of corruption. Right after this, I rebooted my PC and windows did an automatic process of fixing my disk drive. *****

I booted into my NVME and tried to open Valorant which is installed on my NVME. It has me logged out (and this isnt some log out every 30 days thing). So I open my chrome and I'm also signed out of my chrome (which again is not supposed to be the case) and when I sign back in it reinstalls all the different plugins I had previously installed. Also during this same boot, my discord which is set to open automatically, opens and there's a "discord is corrupt" banner over the top 

I have just booted back into my Harddrive to study and this pop up has appeared.

 

Is constantly booting from 2 different drives and writing files to each of these drives while using the other drive causing issues?


*****Clarification for this. I understand that when you fresh install windows, you wont be able to use applications from your previous windows install. THIS IS NOT WHAT IS HAPPENING HERE. I had installed Dota (while booted from my NVME) to my hard drive and was able to play it for a few days.

*another thing that may be brought up: When I fresh installed windows, I installed windows with my Original Hard Drive unplugged from my system so it shouldn't be a windows install issue.