You will lose all progress plotting if you close the application. Also if your computer goes to sleep. The temp files left behind can be deleted, they are useless at that point. Same with farming, it will only farm when the GUI is open. Of course this information is pertaining to the GUI. If you use the command line, I think it is different. But if you use the GUI, it needs to be open to do anything.
Oh, and something else, make sure you pause your Microsoft updates. If your computer decides to update and reboot in the middle of the night, it doesn’t matter which you use (GUI or CLI), your plots in progress are cooked.
I was surprised too, but it’s happened twice now, and all the plots survived. I tested them with the plot check command too. Again – not a good idea, something you should avoid, but doesn’t necessarily kill plots. Shutting your PC down or restarting it definitely will tho!