As far as I can see a game using Proton is installed normally (as if not using Proton) and Proton is separated in a different location.
So am I wrong in thinking it won't erase the entire game and saves (if they are in the game directory) but just update and all will be good?
Unchecking use steam play for all games removes every game using Proton but keeps the savegames as far as I can see as would be normal with Windows. So technically, there shouldn't be a problem even if having to uninstall the Proton version and install the native one.
But, tis always better to have daily auto backups running so that you really won't care much. I like to use Déjà Dup Backup Tool which runs automatically every day to a fast thumb drive (and manually if I choose to).
Currently what happens is this:

After further investigation: game content appears to have disappeared from my HDD. Local Files tab says: "Disk usage: none"
My game save has been deleted, all my progress is gone.
FYI I always found it be the case that windows and linux versions of games don't share save states. Are you using steam cloud to sync the save files? If so, if you re-download / launch the windows version you might still have your saves
If so, if you re-download / launch the windows version you might still have your saves
There is currently no option to do that in the Steam Linux client.
Strangely on my desktop computer the Steam client did not overwrite the Proton version with the Linux version. Not sure what the difference is at this point.
There is currently no option to do that in the Steam Linux client.
There sort of is: https://github.com/Holston5/Native2Proton
Life is Strange mayu or may not work, but you should get your save files. Eithier in the Documents of the prefix or ~/Documents
Nothing extracted yet.
Your system information
Please describe your issue in as much detail as possible:
The Linux version of Life is Strange: Before the Storm releases on 13th September. Currently I have this game installed through the Steam Play feature. What will happen to my existing install of this game when the Linux version is released? Will any files stored in the Proton prefix be automatically removed (e.g. game saves, settings) as the game is replaced with the native Linux version?