The exact timeline hasn't been listed yet, but there are a few assumptions we can make.
It has to be after the Pandorica events.
(Melody is conceived in the TARDIS on their honeymoon).
There has to be enough time for The Church (and Madame Kovarian) to find out about the pregnancy and make a plan.
(Although it's most likely that Kovarian has time-travel capability on her own, "time" becomes a much more flexible requirement).
The Doctor doesn't know about Amy's pregnancy until towards the end of Impossible Astronaut.
Amy then tells the Doctor she was mistaken in Day of the Moon, three months later.
At the end of that episode is the first time we see the "positive/negative" result.
That means that the absolute latest that the swap could be made is between Impossible Astronaut and Day of the Moon (while Amy's on the run).
Plenty of opportunities for a swap to be made, and it's plausible that people out to get the Doctor would know about it by that point.
It also explains why Amy thinks she's not pregnant (three months later and not showing is pretty convincing).
It also matches up with the Doctor's comment about Amy being gone "since America".
The second window is pre-Impossible Astronaut (while Rory and Amy are hanging out at home between adventures).
This is slightly less likely, as it's implied that Amy's only finding out about the pregnancy either during or just before this episode (remember, Rory doesn't know about it).
This makes it more difficult to explain how The Church would know about it as well.
scifi.stackexchange.com/users/963/Allen Gould
It was before the season began because Amy saw Madame Kovarian before the Silence took her.
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The Doctor says in A Good Man Goes to War that it must've happened 'before America'.
He obviously can't know for sure, but I guess that's the information we're supposed to accept as truth for now.
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Amy shoots the little girl in the spacesuit, then three months pass and suddenly Amy's running through the desert and running from Canton and the silence.
There were (presumably) several times
she was alone during those three months,
so I think that's the most reasonable time for her kidnapping to have occurred.
Also, in "impossible astronaut" the Silence instructs her to tell the doctor "what be must know," and she tells the doctor she's pregnant.
Then, after "day of the moon" she isn't pregnant any more, and this is the first time we see the doctor being suspicious of her and concerned for her wellbeing, almost as though he knows something isn't right.
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It happened in the three months that occur between 'Impossible Astronaut' (season 6 episode 1) and 'Day of the Moon' (season 6 episode 2).
She was at least two months along in her pregnancy but could have been as far along as five months.
I can support this logically with facts.
Amy got pregnant on her wedding night in the TARDIS.
The future Doctor summons Amy and Rory to Lake Silencia two months after they got married.
Future Doctor says Amy had gained a few pounds.
(He would have known she was pregnant)
If the Silence had already captured Amy they would have kept her ganger from gaining weight.
In 'Impossible Astronaut' Amy tells the Doctor that she is pregnant.
Three months take place between 'Impossible Astronaut' and 'Day of the Moon' When she is in the orphanage (Day of the Moon)
she sees Kovarian, the eye patch lady.
That means she had already been captured.
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It HAD to have happened in Day of the Moon, because that was the first time Madame Kovarian was introduced, and the only time when Amy wasn't with Rory or the Doctor.
It probably occurred while she was with the Silence, and the one rescued from the Silence was the ganger.
Additionally, Steven Moffat has been quoted as saying that the Impossible Astronaut/Day of the Moon are meant to be prequels to every episode in the current series.
scifi.stackexchange.com/users/751/dkuntz2
In the series 6 episode of  Doctor Who ,  The Almost People , we learn that there had been a swap at some point.    Amy at some point was swapped with a Ganger, a duplicate of her made of the Flesh.  After the swap happened, the Amy Ganger kept seeing the eye-patch woman whenever she checked on the real Amy.  So my question is, when did Amy get kidnapped and replaced with the Ganger?   When did this swap happen?
In series 6 of Doctor Who, when did the Amy swap happen?
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Some assumptions may be made about the timeline for the swap. Some say it was  before the season began because Amy saw Madame Kovarian before the Silence took her,  in the three months that occur between 'Impossible Astronaut' (season 6 episode 1) and 'Day of the Moon' (season 6 episode 2). It must have happened in Day of the Moon, because that was the first time Madame Kovarian was introduced, and the only time when Amy wasn't with Rory or the Doctor. There are few possibilities for when Amy was snatched and replaced by the Ganger. It was either before the season started, between season 6 episode 1 and season 6 episode 2 or it happened in Day of the Moon.
There are few possibilities for when Amy was snatched and replaced by the Ganger. It was either before the season started, between season 6 episode 1 and season 6 episode 2 or it happened in Day of the Moon.