"on the 1099-R is a 1"

The 1099-R issuer uses the code for the money Out. They don't always know what happened to the money after this.

"but I do know the entire amount was put back in the IRA within 60 days"

A trad IRA distribution to your taxpayer would have had required withholding. Have you got the Form 5498 to see the total rolled over? This is for the money In. They would have had to make up the shortfall out of regular funds on hand.

You want to see both forms, confirm it's a rollover (redeposit, not listed as new contribution) and meets the requirements.

Are you using the help articles:

https://accountants.intuit.com/support/en-us/help-article/retirement-benefits/common-questions-form-...