Good news! I got it working. It involved a lot of stripping it down and building it back up little by little, saving and compiling with each step. I had a lot of trouble with HISE crashing and compilation errors, but I got there in the end. Thanks everyone for the help!

One thing that helped me was adding a container to the project and putting ScriptFX nodes for the compiled networks in there so I can open them up easily.

@HISEnberg I tried your suggestion of embedding a compiled network in the clone container, but as soon as I try to do that HISE crashes with no error

Actually, if I add a ScriptFX to the module tree for the network containing the clone node then it allows me to add the compiled node as a child.

Is there a way to work on multiple nested networks without having ScriptFX nodes for them in the module tree?