Hello and thank you for your feedback.
I am glad to know you are using and enjoying FlowCanvas in your project.
The issue seems to be due to the Deserialization in unity (from which where the Type Request error is coming from), which is taking place in arbitrary order and usually multiple times. As far as I can tell, Deserialization is invoked once for each assembly (where the problem is thrown since your custom nodes are not found) and then once again after all assembly definitions are loaded, but I have to check this more thoroughly for whether that is true or not.
Obviously the safest solution of them all, would be to have your custom nodes in the same assembly definition with FlowCanvas itself.
You could for example place the assembly definition file in the “ParadoxNotion” root folder (if not already) and create a subfolder there to hold all your custom nodes. Doing this is still update friendly, since only the “CanvasCore” and the “FlowCanvas” folders are changed when updating.
Would that be an adequate solution for you?