6. If the molecular structure changes, properties should be invalidated, e.g. #2168
7. No, it copies atoms, bonds, residues, formal charges but no properties.
8. IIRC we had a discussion about this before, and properties should be retained unless there are replacement values (the implementation is in core/molecule.cpp)
9. That’s not possible, because at the moment the code (interfacescript.cpp) gives precedence to readProperties

I mean, it’s always better (more precise) if you have the cjson representation to make any specific changes you want. The main point for append and readProperties is to make it easier for plugin authors to do various things.

It’s much easier to use append to implement various “Build” tools because you just add the atoms and bonds to the scene.