Mathematica Kernel will quit due to "a malformed program" and or "syntax error" in the case your running several expressions: it stops to prevent mis-use of the kernel - which could effect "other things" if it were to continue wildly (the kernel by default has access, via your code, to your disk - you wouldn't want a stray program messing your files up).
New users also tend to have problems with Context[] and "already defined variables". (they try to evaluate expressions using "x" but it is already defined, and they become confused that the result isn't what they expected)
Also - installing "malware" or poorly conceived 3rd party software can effect your OS Desktop libraries, causing unexpected closures of applications.
I will not prescribe to 12.1 has new bugs until one has been identified. We have not identified a bug nor shown it to be repeatable, here, yet.
"This happens seemingly at random every 3 hours or so and if I re-evaluate the notebook it usually runs fine."
This is the strongest clue Mathematica has nothing to do with what is going on. I strongly suspect the Mathematica app isn't the only software on your PCs that is effected.
Let me ask: do you have video drivers that update every 3 hours? your using windows10 and have enabled continual updates for drivers maybe?