Actually, we don't know if DELETE really did nothing or if lines are resurrected. Further investigation, with an external tool watching the faulty table every minute, showed that a deleted line was still there at least 20 seconds after the commit. And this line was alone in the table when it should have been deleted.
An example of query is:
I wish I could provide a better bug report but it happens very rarely and we don't know how to reproduce it.
If you think it can help, we kept a copy of the .tokudb files of the table before we fixed it.
To know more about our application, you can read https://www.nexedi.com/blog/NXD-Document.Blog.Optimising.MariaDB.Big.Data. BTW, although we haven't used InnoDB & RocksDB as much as TokuDB, we only got this issue with TokuDB, so we report it here, rather than to MariaDB.
MariaDB 10.1.25 (tokudb_version: 5.6.36-82.0) is the most recent version for which we got this bug.
Priority increased to high because it's an integrity issue.