Breaking an unknown rule had major effect on our Monopoly game, how do we resolve it after we learn the rule?
The rules don't specify how to handle this, but I would fall back on the second following player rolls the dice provision for collecting rent.

When learning a new game, there will always be occasions when a rule is initially missed, and then discovered later. There must be limits on how far back to attempt reconciliation, so adopting a limit already in the Rules is a sensible compromise.

First games should always be recognized as a learning exercise for all players; complete this game quickly, and offer a prompt rematch to assuage any ill feelings. Remember that making the mistake once, in a game situation, is likely the very best way to remember the rule going forward.