What if you symlink the SD card steamapps directory (since its unmounted the mount pount will just be a regular directory on the root filesystem) to your internal storage steamapps directory?
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I seem to have fixed the issue, for some reason the cloud sync was screwing with the installation and clearing out a file related to it fixed it. Thanks for the idea though, on the off-chance this comes up again - because I'm not likely to trust an SD card in it again - I'll look into it
Sounds like your SD card is defective. Try a new card.
Yes, the card appears to be dead, I'm trying to install the game to the internal storage now and it won't install
Have you tried removing the external drive from your libraries in Steam?
It didn't actually show up in the list of libraries, that was my first thought, and that was when I ended up messing with libraryfolders.vdf. Just outright removing that external drive from there had Steam just restore it after a reboot. Removing all the entries from that drive at least stopped it warning me that the game was installed on a different drive.