You'll have to split the 1099-Q and enter it as two separate 1099-Qs.
There's no risk with the IRS, for doing so. The IRS only matches total 1099-S dollars
I would ask the 529 for separate 1099-Qs. If for no other reason to let them know that tax software can't handle a combined 1099-Q and they've done you disservice by doing so.
