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I had to do some forced updated yesterday and run into this issue in RHEL6 hosts, so I've investigated further in the filesystem.
It turned out that there were actually some folders named like build numbers instead of dates. They must have started as normal symbolic link pointing to directory with date, but they weren't anymore.
Here is how you can do a search for those problematic directories in linux/cygwin using bash:
find $JENKINS_HOME/jobs -type d | egrep ".*/builds/[0-9]+$"