Dear RitaB,
Your intuition/memory is correct, to a point. Should you prepare the final 6/30/13 returns using 2012 software, you would have to do a lot of manual tweaking to make it good. Extending the return is not the best option, I believe; your shareholder(s)/client need a current-year K-1 -- under current law -- and, the entity should get this done by September 16, 2013 or, if extended, no later than *early* December, 2013 in order to get a *timely* "all clear" certificate from the state tax authority in which the entity is chartered, in order to include that certificate with its application to that state's Secretary of State for a formal dissolution notice. The SoS's with which I'm familar require such an "all clear" tax certificate -- and you can count on the SoS to take some weeks to finalize its own document.
I also don't believe you should wait for ATX to issue 'solid' 2013 forms before New Year's Eve -- not only because ATX blew it, last year. Your client/shareholder(s) really don't have the option of waiting til next year; they really must report the entity's results within this year -- AND the entity must be dissolved by New Year's Eve, accordingly.
If I were you, I would duplicate the 2012 return as "2013 [client]," and enter the current-year data. If your client's Fixed Assets are as numerous as I infer, you may need to convert the 2012 "4562 Statement" into an Excel spreadsheet, modify it to project the 2013 "short year" depreciation, and use the spreadsheet to inform a Form 4562 with your own totals -- also, to be attached as a Statement to the returns. Such a spreadsheet also will 'inform' the Form 4797 it sounds like you'll be filing.
N.B. A current, short-year return cannot be e-filed. Do you have software capable of changing the tax forms' upper righthand corner "2012" into "2013"? You should do that; it's always helped keep things straight, in my experience. I.e., I just filed a client's final 2013 S-corp as I've described -- and have filed a dozen or so, this way, over the years. NO problems.
VTY, TaxCPANY