This is the same for us. We don't use BPL, mostly because if anything is ever that complicated, we try not to do it at all. That said I know there are organizations that use BPL much more frequently.
We generally also try to use rules for non-HL7 processes for readability. Rules are much easier for us to understand than custom process classes usually.
This isn't an exhaustive solution, but we have found issues when changing message structures because the structures are very briefly deleted before being loaded again. If a host tries to process a message with that structure, it will fail that message.
I would recommend stopping any business host using that message structure. Depending on the criticality of the integration, I would also consider if you needed to let the host finish processing the queue before stopping it.
Our engine usually has the flow: Service -> Process (no DTL) -> Process (DTL) -> Operation
We usually stop the first process and let messages queue there while we make the change. The human part of the process usually takes a <5 minutes, and we accept the small impact when making those changes.