This sounds like the same thing discussed on the user email list at https://groups.google.com/d/msg/jenkinsci-users/h-Eku3NnWLg/le9Xx_a4CQAJ . In that case it did turn out to be connected to underlying filesystem problems. We saw a number of filesystem errors in the logs and other similar problems in other software. In that case, the user was able to run on a different system and avoid the problems entirely.
If you can, try running the same upgrade on a different system with a more stable filesystem. Or reconfigure your environment to make the filesystem more stable. We would need lot more information about the environment and the logs before we could diagnose anything further.
Since there has been a lack of response for quite a while on this, I'm going to close this issue. If you have additional information to help move this along, feel free to provide it and re-open as needed.