Update: I just patched both of the bugs you ran into.
You had it exactly right — maxing that first generator was tipping the upgrade panel into a constant re-render loop, which is what caused the flickering and the dead buttons. That's fixed now. And the bigger one: the game wasn't reliably saving (it runs in an embedded frame here, which was quietly blocking storage), so your refresh wiped everything. I'm genuinely sorry about that run. It now saves on every action, so a refresh can never cost you a whole playthrough again.
Thank you again for the detailed write-up — it made both fixes easy to pin down. You mentioned you might give it another go once it was fixed, so the invitation very much stands. I'd love to hear how the later chapters land for you, but no pressure either way.
Either way, this kind of comment is what makes putting something out there worth it. Cheers.