Note that when you credit something to A3 for 0 miles, it is still counted as credited and you can't easily "uncredit" it to claim again with AC.
What gives you that idea? Have you had any problems with this in the past?
I haven't tried with AC, but with Miles&More it was (at least last year) very easy to retro-credit non-earning segments flown with my A3 FF number. These segments also don't show up on my transaction record with A3.
So my advice to the OP would be, fly everything with your A3 FF number, and retro-credit the non-earning segments to AC. Do you have A3*G? Then it's a no-brainer ;-)