"Taxpayer was told by his investment manager that 5498 would not be available until May."

That's because you have until the Filing Deadline to make a 2023 contribution. Get a copy of the account Statement, and there might be a deposit detail page, too.

"I will have taxpayer provide documentation of when he returned the funds."

Exactly.

"Do I still use the 1099-R worksheet to adjust the payment out of the taxable box?"

You mark the Rollover and enter the details. For instance:

Took 5 x $10,000 gross each time, got $8,000 net each time; only rolled over $8,000 = they forgot to make up the withholding to Gross Up the rollover.