Regarding the uniform-change, one theory is that when Dr. Bashir was initially kidnaped, his evil replacement stole his new-style uniform to wear around the DS9 station, meaning that Bashir would then need something else to wear during his imprisonment. Hence, when the impostor arrived on the station, he went into Bashir’s closet and fished out his old-style uniform and beamed it up to the cloaked enemy ship that was transporting the captive doctor to the prison camp.
Alternatively, since it’s logical to assume that the prison was equipped with replicators so that the prisoners could replicate food, one may assume that the same machines could also have been used to replicate another uniform for Bashir to wear so he wouldn’t need to walk around all day in his jammies or undies. If that were the case, then it’s also logical to assume that those particular replicators had not yet been updated with the patterns for creating the new-style Starfleet uniform, thereby requiring the doctor to replicate an old-style uniform to wear instead.
In either case, the bait-and-switch event could very well have happened well after the events of “The Rapture” when the uniform change occurred and possibly even occurred after “The Begotten.”
Now after reading the above explanations, you might be wondering why a shape-shifting Changeling would need to steal Bashir’s uniform in the first place since he/it could just mimic the uniform in the same way that Odo always mimicked a Bajoran uniform. For this, I propose that Bashir’s evil replacement was not a Changeling at all but rather a flesh-and-blood replicant. My reasons for believing this are as follows:
First, there was an earlier episode in the DS9 series called “Whispers” where Chief O’Brien was kidnaped and replaced by a replicant who possessed all of the real O’Brien’s memories and even actually thought that he was the real O’Brien. The dialogue of that episode’s closing scene then revealed that the replicant would only have discovered his true identity and carried out his evil deadly mission after it was triggered by a code word. Prior to that though, anyone hanging around the replicant would, technically, have been just as safe as if they were with the real O’Brien.
Now since the alien race which created this replicant came from the Gamma Quadrant, it’s very logical to assume that the Dominion gained access to their technology and were thus able to create replicants of their own. They also would have had a very logical reason to replace Dr. Bashir with a replicant instead of with an actual Changeling since the evil replacement was ultimately on a suicide mission. For if the fake Bashir had actually succeeded in blowing up the Bajoran sun, he too would have also surely died in the blast himself. So we need to ask ourselves then if the Founders would really have been willing to sacrifice one of their own for something like this since, technically, doing so would make them guilty of murdering one of their own which is the very thing they judged and punished Odo for.
Assuming the replicant-theory is true, and I believe it is, then even if Bashir had been replaced prior to the “Rapture” episode, the replicant there who operated on Sisko would have, at that particular time, most likely not yet have realized that he wasn’t the real deal, just like in the previous case of the O’Brien replicant. This means that Sisko and anyone else who the replicant may have operated on during this time would have been just as safe on the operating table as if the real Bashir was caring for them.
Any thoughts? Let me know.