In SQL Source Control, if you are working in a dedicated development environment or you switch branches, then you need to get the latest changes from version control and apply them to your development database.

After moving to Flyway Desktop, you'll still need to pull the latest changes from the repository and apply them to your development database.  It's best to visit the Schema Model tab first and make sure there are no changes to your development database that haven't been committed yet.  This way, when you pull the latest from the repository, you'll know these are all changes from the repo that need to be applied and conflicts will be picked up if you made a change to an object and you try to pull a change that someone else made to that object. 

In Flyway Desktop:

1. Visit the Schema Model tab to make sure you don't have any pending changes to your development database.
2. Open the Version Control sidebar and Pull the latest changes from the remote repository to your local repository.  Once you've pulled, the database object changes are now on disk. 
3. Back on the Schema Model tab, toggle to the Apply to database area to apply the changes on disk to your development database.  You will get a confirmation about your development database being updated.

You're development database is now in synch with the all the changes in version control and you can start to continue your work.