TokuDB table stats row count decreases to 1
We looked into it for a while and it looks like this is a regression in Percona. I wasn't yet able to reproduce it outside our own environment, but it started when we upgraded our servers from 5.6.22 to 5.6.28, persisted through upgrading to 5.6.30, and disappeared when we returned to 5.6.22.

The stats decreate was present on both master and slave servers and apparently depended on traffic the database served. I was not able to replicate this on any smaller data nor with any specific queries.