Here are my thoughts on the current developments, there's little structure to it, and I go off on different points...
Why was it necessary for Vermouth to disguise as Scar Akai on the Mystery Train? There were no known FBI agents aboard. Bourbon already gouged Jodie, Camel, and Sera prior to Mystery Train.
Based on the past few chapters, is Vermouth's promise related to protecting Conan? (related, did Scar Akai really protect Conan during the Bank Robbery case?)
Was Team Conan's plan on the Mystery Train really to make the BO believe Sherry is dead?
Okiya has confirmed (in front of Conan) that he is living in Shinichi's house (814.12). We have yet to see Conan acknowledge that Okiya knows that Conan is Shinichi, so let's keep that fact aside for now (for simplicity's sake). Remember that Yukiko and Okiya are acquainted based on the Mystery Train events.
Since Okiya knows Conan is a primary contact (Ran and Yukiko being the others) to get a hold of Shinichi, Shinichi could have been invited into this rendezvous in some form (in Okiya's eyes).
Few more things:
Kir was hospitalized under the pretense that she was Akai's sister (605.5), this statement along with the appearance of Masumi in Japan is something to consider. We have yet to see this fact referenced again. We don't even know if Gin, Vodka, or Kir relayed this information to Vermouth or Bourbon. It is possible Bourbon knows (details obtained from Vermouth in 824.16). Bourbon may threaten her/Okiya in some form, or use the above fact to force other facts out of Okiya or any Team Conan member.
Based on 855.13, Vermouth is being kept out of the loop as Bourbon investigates.
In response to JD. Amuro both saw each other Okiya in 800.11. Okiya was driving his car at the time.
Anything related to Agent Camel is very dangerous - he was supposed to be blown up (603.14), Vermouth is a witness to this. Camel's position in front of the BO and his face being known is negligible (603.13), but it is still something to consider. Vermouth relaying facts between BO's agents is not consistent, let alone her actions but I've always felt that the longer Camel is around, the longer Team Conan has a vulnerability.
I don't believe Kir is in any real danger in terms of the plot. If she escapes/dies, we as readers have only seen one benefit for her return to the BO which was Bourbon being "activated".