Hello @xenoxriar, this issue was transferred to the steam-for-linux tracker because it's regarding Steam's management of Proton versions and not Proton itself.
Steam is expected to refuse to uninstall a Proton version if you have any games installed which are configured to use that version of Proton. The Steam client should tell you if Proton is in use and what version version for individual games by going to you library, selecting a game and clicking ⓘ on the right side for details.
All Proton builds are independent of each other.
proton 3.16x1 2020-02
Basically, the issue here is that when you install a newer version of Proton, say v.5 like I did just a few minutes ago, you can't remove earlier versions of Proton. I know that some of these versions are needed for the proper running of games but versions like 3.7 cannot be removed. I recently just did on my desktop but on my laptop, it displays the "Something unexpeted has happened during uninstallation" (or smth like that, btw steam really should fix that typo).
I'm not sure if Proton 3.16 and 4.11 are needed for version 5 but I can't seem to remove it from my laptop unless I go to the game files and delete it.
Not sure how to reproduce it but installing 4.11 also installed other versions which I can't remove even though I've remove 4.11.