Treat saving as version-sensitive
Autosave and quit behavior can change during Early Access. Before leaving a valuable run, use the game's current save or quit option, wait for any visible confirmation, and avoid force-closing during an active transition.
If a run resumes differently than expected, preserve the version number and the exact sequence of actions. Those details are more useful for support than assuming that an old checkpoint rule still applies.
Source and version note
The topic is independently indexed by shroomgloom.org. Because the current sources do not establish a permanent checkpoint matrix, this guide avoids promising a specific room-by-room save rule.