There is a way to self certify that you are qualified for a waiver to make a delayed repayment of a 60-day rollover requirement for a retirement plan.
You need to submit a model letter, not to the IRS, but rather to the financial institution that is accepting the payment. You can find the model letter here, at the end of Revenue Procedure 2016-47. The financial institution is not obligated to accept your position, but if it does it would change the 1099Rs so that the late payment would go through as a 60-day rollover.
You can find out more about retirement plans and waivers for the 60-day rollovers here and here.
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