You have a fundamental misunderstanding of how IRA contribution limits work.

If this were a Roth IRA then yes, an increase in Modified AGI could result in an excess Roth IRA contribution (subject to excise tax if not corrected timely).

For a Traditional IRA, however, an increase in MAGI does not alter the contribution limit. It simply changes the amount that is deductible on the 1040. An amount not deductible due to MAGI is not excess, is not subject to excise taxes, and does not need to be "corrected". It simply creates (or adds to) tax basis in the IRA which gets reported and accumulated over the years on Form 8606. Sounds like the only thing you need to do is include Form 8606 with the amended return.

Rick