Use a third party launcher like ATLauncher to be able to see the logs of what is going on. To me it sounds like there is too much going on. My game does a similar thing when I regenerate more than 5 chunks with worldedit. It seems like the game is playing normally but it is quietly getting slower and slower until it crashes and disappears all of you progress.
Try adjusting your allocated RAM to 8+ GB and get a 3rd part launcher so you can see what it is that bugs the game out.
I’m not sure what game compatibility with Linux is but.. I just rather download a game and play it instead of fucking around with CLI commands to get WINE or whatever garbage has to be run in order to play video games. But that’s just me. I know better than to ignore someone’s entire question just to suggest what I want.