The book says: "The purpose for multiple stutterwarps is twofold. First, it prevents the failure of a single unit from crippling the ship. Second, it allows the ship to make a single run of up to 15.4 light-years between stars on the outbound and inbound legs of its voyage."
It never mentions anything about ejecting them.
But as you cannot carry a charged drive, you must eject it before the coils begin radiating the whole ship if you reached the 7.7 threshold and watn to keep going with another drive, so it's assumed they must.
And in an article about the bayern (IIRC in a TD, but not sure) they made clear those used engines must be disposed before engaging the spare ones.