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Wonderful news! I'm back in and everything is fully operational!

I figured that the fact none of our solutions were working when they should've might be related to the core problem. Turns out I was right. Firstly, turns out the main drive I was booting from these past years actually was the C drive. By simply booting up with the D drive disabled, it loaded in on the correct user profile and everything was intact. We then plugged the other drive back in while the PC was running, and now everything seems to be back to normal and fully operational.

I'm pretty sure that the 'thermal shutdown' must've somehow changed the boot order, which is what caused the wrong profile to be loaded and probably what prevented the recovery drive from loading (honestly not completely sure on that one). Only thing that's still bothering me is what could've caused the thermal shutdown in the first place. We originally thought it must've been due to dust, as we hadn't opened up my PC to clean it in years. The inside was actually remarkably clean, though, certainly not worthy of randomly overheating overnight. My best theory is that my PC actually got hit with a power surge and just interpreted it as a thermal shutdown.

Regardless, everything seems back in order now. I'll update if anything goes unforeseeably wrong from here.