went back rthrough all the episodes
and the only viable kidnapping moment is before the series as she she's the woman on the door to the ids bedroom before shes kidnapped
also the silence in the bathroom of the white house says there's something you need to tell the doctor
'something you cant and something you should' at the time i assumed the something she cant was the silence but maybe it was that she was kidnapped.
i also think the point he realises amy isnt amy is the convo at the end of the second episode
'why did you tell me you where pregnant'
'i was but im not anymore i mean i thought i was'