Windows acting weird after drive swapping

Hi everyone, I have a question.

On my Lenovo G50 I have a 250GB SSD used as only drive. It has W10 home installed.
I was going to some friends' house and I figured out "heck, why don't I bring some films to watch" so I unplugged my drive from my laptop and, through a SATA 3G to USB 3.0, I plugged it into my main rig. Drive showed up and copying was easy as pie.
I then installed back my drive and left home. I then came back and booted up my laptop and Windows started acting weird. Here's what I mean:
It boots up normally, with the SSD speed and all, has my lockscreen and my login saved but:
-has no desktop
-has multiple broken links on the start bar (mainly files and programs died)
-asked me access to my folders, and I could grant it
-I didn't have access to appdata folders
-after a couple of restarts, start button stopped working as long as Edge
-chrome didn't start in the first place
-factory reset utility died as well
-some icons in my desktop moved, some didn't
-google drive didn't work (onedrive did tho)
-windows account synchronization didn't work
...And many more quirks that don't come to me right now

Now I kinda see why all of this happened: I simply should not have treated my OS drive as an overgrown USB stick as my other Windows installation simply killed that for some reason (I even did the safe device removal!) and now I have this funny thing.
I'm asking you then "why shouldn't mI have done that? Did the pluggate scandalo cause all of this mess?"
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