Besides Weyoun's dialogue still being bugged, I just wanted to note that at the end of Boldly They Rode, it tries to send you to the old DS9 map (which you're immediately beamed off) and doesn't recognise you're on DS9 when you get there. Thankfully this isn't gamebreaking as it jumps ahead when you talk to Kurland.
Also, while the final battle uses the new DS9 exterior, the old exterior is still used for Operation Gamma (I presume this is a scaling thing, as the same is true for sector space).
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