I haven't tried this yet, but it seems risky. The case I'm thinking of is instrumenting simple VO classes with JiBX. These VOs are going to be serialized over AMF and possibly other schemes. Can anyone confirm or deny my suspicions that doing behind-the-back stuff like bytecode enhancement might mess something up in general, and provide some background information as to why? Also, I'm interested in the specific case of JiBX.
Behind the scenes, serialization uses reflection. Your bytecode manipulation is presumably adding fields. So, unless you mark these fields as transient, they will get serialised just like normal fields.
So, provided you have performed the same bytecode manipulation on both sides, you'll be fine.
If you haven't you'll need to read the serialisation documentation to understand how the backwards compatibility features work. Essentially, I think you can send fields that aren't expected by the receiver and you're fine; and you can miss out fields and they'll get their default values on the receiving end. But you should check this in the spec!
If you're just adding methods, then they have no effect on serialisation, unless they are things like readResolve(), etc. which are specifically used by the serialisation mechanism.