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In season six's "Day of the Moon", the Doctor et al. show up to rescue Flesh Amy from the Silence after she is kidnapped from the orphanage.

When they step out of the Tardis, the Doctor calls our attention to the ship's resemblance to the stranded spaceship which posed as a second floor flat in the season five episode "The Lodger":

"Oh. Interesting. I've seen one of these before. Abandoned. I wonder how that happened."

We know that the ship in "The Lodger" is a Silence ship.

However, was it the exact same ship in both episodes?

I'm inclined to think they are. If they are then did Amy's proximity have anything to do with how much difficulty the Tardis had trying to land and staying put?

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Unknown

As far as I'm aware, this has not been explicitly confirmed one way or the other, and you can make a decent case for either side.

On the one hand, Moffat's comments (cited in my answer to your last question) seem to imply that the ships are distinct, or at least that there's a non-zero chance of them being distinct (emphasis mine):

Those were Silence ships. That's how they arrived on Earth, and where they hung out and had parties and games of forget-me-not (is that a game?). So the one the Doctor found in The Lodger was an abandoned ship from the Silence occupation that was in the Earth's past

Doctor Who Magazine #475

Also telling is that the Doctor doesn't seem to think they're the same; note his word choice (emphasis mine):

Doctor: I've seen one of these before. Abandoned.

Doctor Who Series 6 Episode 2: "Day of the Moon"

And really, given the scope of the Silence occupation, we would expect the Silence to have multiple ships.

On the other hand, there's some circumstantial evidence to suggest that they are the same:

  • As I noted in a comment on my prior answer, the Doctor's words in "Day of the Moon" are telling (emphasis mine):

    Doctor: I've seen one of these before. Abandoned. I wonder how that happened? Oh, well I suppose I'm about to find out.

    Doctor Who Series 6 Episode 2: "Day of the Moon"

    There are two ways we could interpret this line, and one of them implies that the Doctor is about to find out how this specific ship is going to get abandoned1. Because he causes it to be abandoned

  • The last we see of the "Day of the Moon" timeship - that is, partially exploding2 and with the entire crew dead - leads quite naturally to the condition we're told the ship in "The Lodger" ends up in:

    Hologram: The ship has crashed. The crew are dead.

    Doctor Who Series 5 Episode 11: "The Lodger"

    But, if the ships aren't the same, it requires some mental gymnastics to explain how 1960s humans managed to board a timeship, kill the crew, and cause it to crash. It's not impossible, of course, but it's marginally less plausible

Unfortunately, that's about the best we can do.

The question of Amy

There's no indication that Amy's prior (future?) interactions with Silence timeships was responsible for the TARDIS' inability to land. It's certainly a possibility, but the TARDIS has also demonstrated fussiness about landing in areas that are bound up in time travel (see the Doctor's first attempt to land in 1938 New York in "The Angels Take Manhattan", for example), or around time loops (see also "The Pirate Planet"). While it isn't impossible that Amy (or the Doctor himself, for that matter) is a contributing factor in this case, it seems unlikely; in the grand scheme of things, it just isn't that hard to futz with the TARDIS' ability to land.


1 The other interpretation, and the counterargument to this point, is the line I emphasized before: the Doctor evidently doesn't think the two ships are the same, or at least doesn't think that immediately. My counter-counter argument (such as it is) is that it's not out of character for the Doctor, especially the Eleventh, to contradict himself mid-sentence

2 TODO: come up with a novel "TVTropes will ruin your life" joke

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