"No, why?"

Because you seem to be focused on the 1099s.  The 1099s in the software don't get transmitted to the IRS so there is no reason to use them.  Just enter what the actual receipts were for the year on schedule C.  You can always attach a note to the return stating the reason for the income to be less than the 1099s but the IRS isn't going to read it.  Just leave a note in the file in the event the client gets a notice somewhere down the road about the timing issue.