If there’s a difference, then you can force the branch’s schema to be updated, as described in my #2 above. From then on, as long as you have that branch active in the IDE every time that you use the IDE to change its linked database, the IDE will keep both copies of the schema in sync.
Edit: if you use a different branch to change that database’s schema, then you’ve bypassed that automatic synchronization. This may result in surprising warnings later on. I suspect that you’ve experienced this already.