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Ok, let me back up a little. Don't worry, things will get fixed.
The 1080ti is a Pascal card (the architecture of that series). This has implications for drivers and performance.
First: when you installed Pop, did you select the installer with nvidia support? There are multiple installers, but the one you want is the one which explicitly says it is for nvidia.
PS- if you don't want to worry about Linux for the moment, or are too nervous to continue, letting windows do its fixes should recover you to where you were before the Linux install. Just make sure the Windows drive is selected for boot in BIOS. I'd say stick with it, but it's your call.
I installed "casper_pop-os_22.04_amd64_nvidia_debug_1131
And I would love to let Window do its fix but it isn't working. It fails and when I select Continue to Windows anyway (or whatever it says) it just goes back to the repair screen.
This is an old version, and "debug" normally suggests this is not a stable build.
~~The most current nvidia version on
system76.com/pop/downloadis 24.04 with the filenamepop-os_24.04_amd64_nvidia_23.iso.~~ Ah but it is not compatible with Pascal cards.And the Windows drive is selected as the boot drive in BIOS?
Yes. It doesn't give me the windows repair if I have the Pop installed drive set as the boot drive, it just goes into Pop
I edited my comment above because there might be something else on the Linux side. Pop 24.04 is explicitly incompatible with Pascal cards, and System76 do not make old builds explicitly available. I'm not sure if 22.04 was compatible with Pascal either, so that may be your entire issue with drivers on the Linux side. From what I can tell, the nvidia package itself requires a 16xx series card or newer.
Edit: Yes, it looks like nvidia have dropped support for Pascal in their official Linux driver just 2 months ago. And that's why Linux people tend to hate nvidia. :)
This also means that the Linux bootloader was already on the second drive, and the bootloader on the first one should not have been overwritten. So it isn't clear what happened to Windows unless there were other runs of the Linux installer which had the bootloader location set improperly.
If it were me, I'd start experimenting with restoring the system to the original configuration entirely (i.e. wipe the second drive so it's blank, and see if the Windows repair process goes differently). I wonder if Windows cannot recognize (or won't recognize) what is on drive 2, and instead of telling you that, it just errors out.