I agree your point. But this is the behaviour of any merging tool, it should show the 'differences' where they are present (Source/Target) and user can merge the differences to the target. But in this case the confusion arises because we use a tree view display instead of the normal text merging display. The current design considers the source as well so that the user gets a clear idea of the exact differences before syncing. Changing the current behaviour may introduce new confusions. But honestly we did consider all these before implementing this design.