This is not a limit of Processing, this is a limit of Java itself, so nothing can be done for that.
Well, you can do something, actually: just move some code from draw() to separate functions. The limit is per function, not per class.
It is really a better practice anyway: it makes the code more modular, easier to maintain, to read.

I re-read your message. Do you mean you generate the .pde file? What is the advantage over using core.jar (and pdf.jar+itext.jar) directly from your Java program?
Breaking up the generate code can be more tricky. Perhaps you can look at the generated patterns and see if they can be factored out to some functions.