Thank you for digging into this and for the theory, which is exactly the kind of thing worth writing down.
I went and checked the loan code specifically because of your comment, and loans do get added to the principal correctly; nothing gets wiped or forgotten when you pay back down. So that part I can rule out.
What I think you were seeing is the refinancing. Your log shows you signed the 3% tier, straight down from the starting 10% you skipped the 6% one entirely. That cuts the minimum payment to roughly a third of what it was, instantly, on whatever the debt happens to be at that moment. On a debt of a few million that is very easily "several hundred thousand" lower than the number you had in your head, and it happens the moment you click the button rather than gradually. The game tells you the new rate but does a poor job of connecting it to the payment you're about to see, which is on me.
If that doesn't match what you remember particularly if the payment looked wrong before you refinanced I'd really like to know, because then it is something else and I'd want to find it.