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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.