I am not sure if currently there is a way to get around this, but each time after updated the forum, the custom agreement I put there were all gone back to the MyBB default.
It would be nice to have the old agreements stay in place after each update.
If you make core edits you need to note them down and reapply them after the upgrade, or create a separate language pack and update that with the new changes every time you upgrade.
It might be better if the agreement was an actual setting in the Admin CP, that way everyone's adjusted agreement wouldn't get wiped out.
It didn't make sense for that information to be in there, since all users registering should read the board's rules in full before making the account, thus the need to edit the agreement.