Her nanites ought to have been disabled by the field, why wasn't she affected? Is there an in-universe explanation that I missed?

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They adapted the cloak to disable the replicator nanites. The cloak only alters things on the external surface of the puddle jumper normally, it doesn't extend a field inside the jumper itself. The field initially materialized around the ship and she stayed in the ship, so she wasn't exposed to it then. When she left the ship, the replicators had adapted to the field. So Weir's nanites could have also adapted to the field, as they were in communication with the replicators.

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    The hallway in which Oberoth and Weir were "fighting" was one that the SG team was using for their heist. They ran past Weir and Oberoth on the way back to the ship. So that hall must have been inside the field perimeter. In addition, at that point the replicators had adapted to the field anyway, so Weir's nanites may have adapted too. – user1027 Mar 27 '11 at 5:06
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    Thinking more about this, my initial answer didn't make sense. We see replicators pierce the field for a little bit as they start adapting to it. So being within the field must cause the nanites to become inert. I've edited my answer appropriately. – user1027 Mar 28 '11 at 13:15
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    The field only disables replicator cells that pass through it, she was always inside it so she was never disabled. When the field was created it started around the ship (didn't grow from the center of it) and extended downwards, killing replicators that would have been inside the field, but not wier inside the ship. – Jonathan. Apr 30 '11 at 22:42
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    @Jonathan That's what I thought too, but we saw replicators start to get through the field, getting further each time they adapted. So either the field has a really thick boundary, or anything in the field is affected. – user1027 May 1 '11 at 2:57
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    @Keen Your original, un-edited answer was correct, now it is not. As said in Jonathan's comment, the field disrupted the replicators that passed through it - it didn't immediately shut them down. The instability from the disruption was reduced with each iteration, lengthening the time before complete failure occured (hence appearing to "push through"), but the disruption itself was a one-time event as they passed through the thin field. – Izkata Nov 18 '11 at 0:56

The cloak field might not propagate through the hull of the ship, and the generation is likely an external grid.

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