From what I've seen, source code generation works best if:

1. You don't have any reason to modify the class's code once it's been generated, or
2. You're working in a language like C#, which allows you to make classes span multiple files. (You can have one file with auto-generated code, and another with your contributions)

Based on your question, I'm guessing neither of these is probably true. While I haven't personally done bytecode generation, I've noticed that some well-used tools like GWT have chosen that approach, so it's probably preferable.

However, I'd ask a colleague to listen to what you're ultimately trying to accomplish and see if there's not a better way using more standard Java practices.

From what I've seen, source code generation works best if:

1. You don't have any reason to modify the class's code once it's been generated, or
2. You won't have any reason to re-generate a class's code once you've modified it (scaffolding approach), or
3. You're working in a language like C#, which allows you to make classes span multiple files. (You can have one file with auto-generated code, and another with your contributions), or

Based on your question, I'm guessing none of these is probably true. While I haven't personally done bytecode generation, I've noticed that some well-used tools like GWT have chosen that approach, so it's probably preferable.

However, I'd ask a colleague to listen to what you're ultimately trying to accomplish and see if there's not a better way using more standard Java practices.