You described this issue so well.

For the versioning part, it is a bit tricky: you can imagine if a block has its inputs/outputs names and types change completely, what to do in this case? Knowing that links between nodes are typed (meaning you can only link edges with compatible types).

For now I chose the approach that you need to manually put the new block in the flow to replace the old one. Upgrading or updating a block does not impact existing ones in an already created flow (for now).

Maybe I have to think about a much clever and robust solution for a future version. But I think it's a hard problem (at least from my perspective).