Not possible to update the contract type check box after the upgrade.
In R12.1.3 the check boxes on the contract type don't exist - it's an added feature in R12.2.4. When the instance is upgraded it takes the current settings for existing contract types and sets them by default, meaning all are checked and if the the pre-upgrade contract type doesn't have the Contract Terms value checked the upgraded one doesn't, either.
The problem is you can't change them after that.
Is there a workaround? Is it safe to directly update the table to toggle those flags (check boxes) or are there dependencies that make that difficult?