Proton takes over both package management and user preferences. This means on initial installation your whole atom configuration is changed with no recourse to revert.

Proton should have a very clear warning about this on first install, with an option to back out and instructions on how to backup your current configuration and/or run proton in a new atom home folder.

PS: I feel like this issues has probably been mentioned before but I couldn't find anything about it. Sorry if it's a duplicate issue.