I put in an issue:
http://code.google.com/p/chromium/issues/detail?id=169417
one of the developers got back to me and said:
I can't remember the release numbers off the top of my head, but at some point when we turned on correct partitioned storage, there would have been one-time data loss. This was done before packaged apps rolled out officially to stable. If the loss of data happened across an chrome upgrade, then I would say it's expected. It certainly shouldn't be happening anymore.