After playing for a bit more it looks like my issue was definitely not using Save & Quit. I didn't realize autosave hadn't yet been implemented. I had encountered a game freeze (tried to use the Time Freeze store gadget to get around Nabooti electric fence bug) and so had to close via the "Abort" popup which doesn't allow saving. Recently I've just been using Save & Quit from the menu to make a save every few minutes and that has worked so far.