Keeping all data (including state) in the DB allows you to develop manipulation programs in whatever language you like. Concurrency will be handled by the MySql server process, so it won't be an issue to you for what server state consistency is concerned.

As for data consistency, you really have to dig into your code looking and take countermeasures regarding possible critical races in UPDATEs. This could be achieved with a custom "locking" mechanism (via an added column, for example), but understand that a lock by a program which is about to die makes the locked data "read-only" virtually forever. Another quick solution would be replacing UPDATEs with REPLACEs.