Saving changes in the compare editor doesn't work if the swap sides preference is activated (i.e. "Swap left and right view").
If the compare editor is closed without saving it asks for saving but it is not saved if "Yes" is selected.
Also Ctrl+S doesn't save the performed changes.
Saving works without problems if swapping is disabled (i.e. "Swap left and right view" is not selected).
The "Swap sides" feature was introduced with eclipse 4.6.2.
Please see https://bugs.eclipse.org/bugs/show_bug.cgi?id=512771 for further investigation results.