When a merge is done for models stored in an SCM system such as Git or ClearCase, it is important to understand how to commit the merge results both to properly record the merge in the SCM system and to save the resulting model in the local workspace.
The important thing is that it is necessary to press the Commit button to save the results. It is not enough to exit the merge dialog via the Close button or to close the dialog using the X button in the top-right corner of the window.
Git users should not be confused by the name of the Commit button. It has nothing to do with a Git commit, and simply means to finish the current merge session.