Your system information

• Steam client version (build number or date): 1.0.0.59-1
• Distribution (e.g. Ubuntu): Arch Linux
• Opted into Steam client beta?: [Yes/No] No
• Have you checked for system updates?: [Yes/No] Yes

Please describe your issue in as much detail as possible:

If a game that features native Linux support is installed from windows, the following issues appear:

• Steam does not recognize the game was installed from windows, and as a result
  • Tries to update the game with Linux files (and thus needs to have an integrity check from Windows)
  • Does not allow trying to start the game with Proton
  • Does not allow updating the game with Windows files

I understand this SUPER was never an intended use case of Steam libraries. I only linked my library on an external drive to install windows-only games on it from Linux, and then discovered this. Some kind of support for this use case would be appreciated, though, even if it is just breaking the ability to link a Windows steam library to a Linux steam install (which wouldn't be preferable but would prevent anybody from breaking their games like this).

Steps for reproducing this issue:

1. Boot steam on windows, install a game which has both linux and windows native releases.
2. Reboot to linux
3. Start steam, see the above mentioned issues occurring.