How did they know which O'Brien was the original?

Question

In the Deep Space Nine episode "Whispers" Miles O'Brien is apparently replaced with a replicant that was supposedly programmed to interrupt some peace talks in the Parada system. At the end of the episode, the replicant is shot and killed. But how did Sisko and team know that the O'Brien they went home with was the real one and not a replicant?

According to Bashir:

"There was no way to prove he wasn't you. He passed a physical exam with flying colours, and he sure knew his way around the station."

If they couldn't prove that the replicant wasn't O'Brien, it seems strange that Sisko and the crew would blindly take the Paradan rebels at their word, rather than trust in their own tests and interactions.

Answer 1

In this particular instance, the Paradan government are cast as the baddies with the plucky rebels as the goodies. The Federation appear to have high level contacts on both sides of the fence and when they receive credible intelligence (from the Rebels but via a government source) that O'Brien has been abducted and replicated, there's no particular reason to disbelieve them.

They take sensible precautions to isolate him from key systems, to check his memory and perform a complete physical examination while they try to work out if the Paradan rebels are telling the truth. Their suspicions (that he's a copy) seem to be confirmed when the fake O'Brien begins behaving more and more erratically, finally culminating in his escape from the station.

Unbeknownst to them, though, the reason for his erratic behaviour is that he's discovered their attempts to shut him out of their key security systems. The ultimate irony of the episode is that the fake O'Brien isn't acting strangely at all. The senior staff are the ones who're acting strangely and the O'Brien replicant is acting perfectly normally.