So it sounds like you aren't filing original returns, but amended returns because IRS has assessed taxes based on substitutes for returns it "prepared."  Which means they had some indication of positive income, maybe the rent was reported on 1099's?  

If that's the case, you need first to know what numbers IRS started with.  I'm not sure software is the most efficient way to handle this.  Is there just Schedule E rentals to deal with, or other issues?  Are the rental losses greater than the net income from other sources?  Good luck -- at least the client didn't come to you in mid-March, as often happens with deadbeats.