As far as the software is concerned, a strict relationship of part to balloon always holds true that I'm aware of. But what you consider as identical parts may differ from what the software considers is identical. For instance, if you have assembly cuts it may consider the part unique compared to it's identical "part" because it has been altered at the assembly level.
This has been a headache in the past on large weldments I've worked on. Consquently a two-tier approach to large weldments was developed to keep machining operations in a separate model from the weldment assembly. So, an assembly of large parts and weld features was merged into a single part file upon which machining operations were modeled in. It's both representative of the real world part and keeps the welding drawings separate from the post weld machining drawings, as it should be. Finally, BOM issues and assembly cut problems went away.
What do you hope to accomplish by having duplicate balloons?