"will the tax on the required minimum distribution that was returned to the account show up on the form 5498"

No one "returns" the tax, once it is paid to Fed/State. It's just part of any prepayment, withholding or estimated payment for that tax year.

The only way you avoid that is the taxpayer makes up the difference in their redeposit. That's why you examine if the redeposit (rollover) of an RMD (which had to be made by the end of August) is Gross or Net. If Net, that amount is a partial taxable distribution.