The territory ownership for worlds that are merging is not transferred with the merge - only the destination world retains territory ownership (and those worlds do not experience downtime at the time of the merge, so any wars on destination worlds can go forward with no interruption). Territory owners should be reimbursed for the land ownership lost in a merge.
War declarations should not be possible on the worlds set to merge once they are confirmed for merge either, so if you were able to declare after the messaging went up, let us know. If this war was declared and not already canceled when we posted messaging on the world, let us know too.