Hello David
Hmm, that’s an interesting scenario. You are correct in your statement:
However, when you connect two MST regions and a CIST root bridge is chosen, this connection should not change the regional root bridges you have within each MST region for your internal MST instances. You must keep in mind that the port roles for the internal MST region are not the same as the port roles in the CST. Regardless of whether SW1 or SW2 is the root bridge for the internal blue MST region, because SW5 is the CIST root, one of the two Gi0/2 ports on SW2 or SW3 will become a root port for the CST. The roles you have in your final diagram are those of the blue IST, with SW1 as the root.
Now my question here is, how did you determine that SW2 became the regional RB after the two regions were connected? Did this actually change once you connected them? By definition, the election of the CIST root does not directly affect the regional root bridges within each MST region. The regional root bridges remain as they are, determined by the MST protocol within their respective regions. The CIST root bridge provides an external reference for inter-region communication only, and does not alter the internal MST instance topology.
Can you share with us more info about that root bridge change in the blue IST and how and when it takes place?
I hope this has been helpful!
Laz