Total amount goes on Form 1040, LIne 5a.  Taxable amount (zero) goes on Line 5b.   If an IRA, then lines 4a and 4b.  IRS sees this about 100,000 times a year and the software should let them know that it was rolled over.  Likely, this was not a trustee-to-trustee rollover; your client received a check, then deposited it within the required time in the new account.  IRS will also receive a 5498 from the new trustee, showing the amount received.  The 5498 from the former trustee is worthless, but the 1099-R from them is not a problem.