"Do I change the taxable amount on the 1099?"

Perhaps you are confusing their Net and their Distribution?

What code(s) are on the 1099-R? Was this a Trad IRA? Did the remainder go to the same type of account (you should be able to get the account statement for that deposit or the Form 5498)? How old is the taxpayer?

You have a partial rollover. The part that wasn't included will be taxable in most cases; unless you know they have basis in that account?