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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.
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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.