MST works by sending a MD5 digest which is used to compare the MST configuration. Name, revision and instance to VLAN mapping makes up this digest whic his compared between all switches.
Adding another instance or moving a VLAN between instances will trigger Topology Change. When the change is done for a while there will be different MST regions because they don't agree on the mapping. The switch with lowest priority for MST0 will be the CIST root. Switches in different regions will have a single port elected as root towards that region, it will be the switch with lowest external cost towards the CIST root. Other ports will be blocked.
I would suggest to only do these kind of changes outside of production hours. Also see this thread which contains a lot of useful information: