I've only had the files necessary for operation in the sys folder. I only ever notice config.g isn't there when I go to edit it. Sometimes I'll realize I forgot to do something after it goes to reboot the board, so I'll wait, then go back to system editor and see the file is gone.
I don't know if this is relevant, but if I reload the page (like if it's on a tab and my mac has to reload the tab because I was doing lots of other things) the board will repeat the last few instructions sent to it. Even if it is printing, it will interrupt the print to home and calibrate. This happens every time on safari, and a little less frequently on firefox.
Basically, once it's all dialed in, the board works great, but interacting with it in any way leads to unpredictable results. Still nowhere near as bad as octoprint though.