Sorry, but why even use a complex and bulky structure like the state_machine if it is clear it can't work as it is without breaking. An idea would be to store the version number for each saves and do changes to your structures when loading a game depending on the save version and the current version. The current system will just break the help system each update and at some point break saves overall, without a way to deal with this situation it will end badly.
Edit:
it appears it already breaks this time as e.g. claire_event_delay is never set, so it never changes from her quest34 to quest 35. Same with Lexi quest 6 to 7. So far I can only progess using the console. Defining states ahead to not outright break and then later redefining them at the start of the game is a total mess.