Apparently my long text did not go through. So I'll start over here.
I built a PC over the weekend, installed Windows on my HDD and pop os on my M.2 SSD. I kept having some issue that a itracked down to: when I restarted from Windows, bios and everything else could not see the SSD as installed. But if I shutdown and booted up, it shows up.
I figured that was enough to reinstall pop os, and just shutdown instead of restart to switch OS. Now once I did that and booted up windows, some diagnostics ran that I think overwrote the Linux boot files with windows boot, so now I can't launch pop os, only windows.
I'm beyond frustrated and just want to be able to work on school stuff instead of installing OSs over and over. I wanted to avoid installing with the other drive removed because getting the SSD in and out is a pain, but will that fix things? Should I instead have /root of pop os and the C drive of windows on the SSD and then /home and a D drive on the HDD? What's the best way to stop wasting my time with this and move on with dual boots?