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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?
Windows will absolutely wreck your Linux boot everytime it boots from my experience (I'm exaggerating the technical side a bit of course). The way I got my dual boot under control was to install easyUEFI on windows and from there to set Grub as Launcher: https://www.easyuefi.com/index-us.html Look here for a guide: https://superuser.com/questions/1247300/how-to-make-uefi-bios-start-grub-not-windows#1248255
Also later make sure windows has Fastboot and energy saving disabled or it will lock down your write access for any disk that is installed in your PC.
I think installing each OS with only one drive in the machine might help. That way, both will be fully contaned on their own drive (including their boot partitions and such). I've heard people say that makes dual booting much smoother. Then just make sure that grub can find Windows and have the linux drive as your boot drive. Shouldn't have to remove any drives after that hopefully.
I'll try that. Do you think it matters that I had the SSD in with this Windows install, and I can just remove the HDD when I try to reinstall linux? Or should I start from scratch again?
Also, this is my first time using a M.2 SSD, I assumed it would just be like using a regular SSD, but I don't understand why even when I only had Windows installed it would only show up after fully shutting down and not when restarting. Is this normal behavior for a M.2 SSD, or did I mess it up when installing things, or did I maybe get a faulty drive?
If it were me, I'd start from scratch just to be absolutely sure. I'm no expert though. It would just nag at me the whole time that something is going to go wrong if I didn't redo the whole thing.
Regarding the M.2 drive, I can't give advice. I've only dealt with them once or twice when installing and they worked like any other drive. Nothing funny when shutting down or rebooting.