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My guess is that the build deletion got interrupted by some Windows process (e.g. your antivirus or search indexer) locking a file. Hence the build was still in memory, but no longer (in the expected location) on disk, so it could not be loaded again.
No build.xml file, so it cannot be loaded. You should see a warning logged about this on Jenkins startup.
To the best of my knowledge, when you delete them manually. Their existence means the deletion of a build failed.
That a failure to delete the dot-build directory causes Jenkins to keep the build in memory seems weird. Should probably be filed as a bug if it's not already.