Hello. I have the same problem and i found it after playing a long time (15-20h). I did do the puzzle in the bug Gym and I have a chapter 6 quest ongoing.
I tried to load a old save but did not manage to (probably my fault, i must do smth wrong).
Do you now if it will patched someday ? Honestly right now, I do not have the motivation to redo everything. If it will be patched, I will wait. Thanks you.