I think the main problem is when MP tries to read the database and the other MP is currently either updating it or just reading it, it locks it so the other MP cant access it. I'm having this problem on my setup, i'm always getting no series found and if i check my error logs i see much of messages about the database being locked.
That's absolutely true. SQLite simply hasn't been designed with shared remote access in mind. Furthermore even other DB's might suffer from transaction deadlocks. Therefore a shared DB setup won't work if more than once instance of MP is accessing it at the same time.
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