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but wait -
The Doctor said the TARDIS stabilized the Flesh so the gangers were real people now, yeah? But then five minutes later he sonic-melted ganger!Amy. ??? ... I assume that was because the other gangers were dupes of real people who were dead, but real!Amy was still alive back in the ... weird MRI-tube birthing-chamber thing she's apparently been in all this time, so ganger!Amy was somehow not stabilized? Anyone else have another explanation?

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I might have figured out open ID
I think the stabilization thing the TARDIS did was mainly to keep the gangers from going all gooey faced as they did intermittently after the solar tsunami, dropping glops of themselves into the bathroom sink as ganger!Jen did right after she wandered off with Rory and drawing on walls with their own substance as ganger!Jen did sometime during The Almost People. No more wibbly wobbly, Flesh-weshy in other words.
What I got out of the end was that the Doctor had big plans to dump Amy and Rory somewhere, figure out what was up with Flesh people (specifically how to dissolve them) then go deal with ganger!Amy and rescue the real deal. I never got the feeling that the TARDIS stabilization was supposed to make gangers human, just able to pass. Ergo, the sonic should be able to dissolve a ganger (stabilized or not) once the Doctor knew how to program that function.
What I totally missed is whether the Doctor knew Amy was a ganger before he hit the monastary, when exactly he figured that out and how on Earth she got to be one in the first place. I'm guessing the alternating positive/negative pregnancy reading on the TARDIS monitors was his clue and the now-you-don't-see-or-remember-them aliens had something to do with her gangerness.
Does that make sense, or do I ramble?