"IRS did not accept the partnership returns, but they didn't notify my client until three years of returns had been filed"

This doesnt make any sense.    They would have been rejected electronically, or returned if sent in by mail if they hadnt been accepted.  

Im not sure youve got the full story.

But, no magic way to change a 1065 to a 1120S.  Be sure you get a large retainer for this, sounds pretty messy.