Yep.. happened to me too. Want to make a video about it. I had to go back on every corner of my game changing from local to temporal when I had the chance (whenever someone asked you a yes or no answer and stuff like that). I also turned many of them to flags, and it was a nightmare because I had to keep track of them on an excel ha ha ha. This took months to fix. I also used a global variable that was shared among minigames or numbers that could be reset on init screen.
I discovered this issue when I realized the variables were rewriting themselves (I didn't know you could check how many active variables the game had).
I feel you, it was one of the most terrible feelings I had while scripting the game, because I knew the only "fix" was going back and redoing most of the interactions and stuff. A valuable experience that will not repeat itself. Local variables can turn your project into a nightmare, and temporal ones are your best friends (whenever you can use them of course) alongside with flags and using global variables multiple (and I mean a LOT) whenever you can.
God I could re live the feeling just reading your post. I shared my experience with my Kickstarter backers, but a proper video showing this tips needs to be done ha ha ha.
Im sorry it happened to you, but I also know you will never, NEVER ignore that issue in the future. The trauma can be huge ha ha ha. Cheers and best wishes on your project!
PS: Deactivate the "view connection lines" as well and get used to work without them, no matter if you are working on an old pc (like I did) or a PC master race moster machine (tested in a few). By showing them on your project you will start getting unbearable slowdowns with everything (including simple stuff as writing dialogue) and you won't be able to even select scenes anymore ha ha ha. "Flies away"