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I got into a state where, after a restart, two files appeared as incoming deletions but they were never deleted. What is strange is that I did an update before noticing and the files got deleted. I then resynced and the files appeared as incoming additions. After updating I restarted (after installing a new build) and the files appeared as incoming deletions again. The files were CustomHashtable and TreeSelection in the org.eclipse.jface.viewers package. A synchronize fixed the problem.
I am unable to reproduce this. Also,subsequent syncs fixed the problem so it is not severe.