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Created attachment 268638 [details] test repository The comparison editor can loose tracks of the changes in the editor. In this case, the editor doesn't become dirty when diffs are accepted or rejected and it is not possible to save the changes. It happens when the conflict group is fold up. To reproduce, import the given repository, checkout branch master and compare extlibrary.ecore with branch right. In the comparison editor, fold up the "Conflicts" tree, then unfold one of the other trees and accept or reject a diff.
After further investigations, the issue comes when you try to accept or reject a diff while there is nothing displayed in the ContentMergeViewer. When a diff is selected and you fold the group containing this diff, the CMV is emptied. After this you can select any other diff in the StructureMergeViewer (by single clicking), the CMV remain empty. If you click on accept or reject, you will ran into the bug. If on the other hand you double click on a diff in the SMV, the CMV is filled and you can accept or reject the diff without bugs.
This is still happening in the latest versions