Here's the steps that needs to be done...
Stop SOI (at least manager and UI server)
Run the following two queries on the database:
delete from ca_ssa_tags where tagname like '%synchronization.inprogress%'
delete from ca_ssa_tags where tagname like '%synched.pending%'
Clear the ActiveMQ data store by removing all files in SOI\apache-activemq\data\kahadb\
Restart SOI (manager first, then UI server)