Sorry to hear you're experiencing these problems and needing to go back in the game to go forward. This one is probably due to a confluence of factors, some of which are my fault. In the first instance, Inceton's lead coder is on leave right now for personal reasons. They will be back soon, but this has definitely had an impact, as he is brilliant at spotting missed things and making sure the game runs smoothly, as well as correcting my errors, where I focus so much on writing the main script that I miss editing errors or logging branches correctly. This was mentioned in the release notes for the game on Patreon, along with a request for players to bear with us if there were more issues than normal. However, I know those release notes are not typically mentioned here.
For my part, I have been so focussed on trying to get the dialogue and story for Zoe and Megan's sections right, that it's become apparent I started overlooking things like placing branch and coding requests in my script. I sometimes get tunnel vision this way, and the confluence of rewriting sections I wasn't fully happy with, along with a difficult summer means I do seem to have forgotten to put in requests where I needed at times. I need to be more on the ball, and hope to be so going forward now we're finding a new rhythm after the summer break.