How can I transfer annotations from a PDF to another in iPad? I know there are a lot of ipad/pdf questions out there, but one of the things I don't see explicitly answered is the ability to transfer/merge pdf annotations from a pdf to an update pdf (only pages added). 

Seems like a unpopular use-case for pdf annotation, but this is the case with alot of legal related documents. The court allows for access to the pdf, of course the lawyers need to take notes on the pdf, exhibits are added, then the court sends lawyers an email to download an updated pdf.

Anyone know of any ipad software that can store the annotations outside the pdf or even better merge the annotations to an updated file? Pages are just added to the end of the pdf file.
GoodReader can't do this and GoodReader suppport is unaware of a product that can, since they operate in this space I assume there isn't an iOS app for this.

GoodReader can display PDF files, add annotations to them, and save those annotations to that specific file. Unfortunately it's not able to edit the content of a PDF file, merge files or create new PDF files.

On a computer, the software that does this is Adobe Acrobat Pro. Unfortunately I can't recommend an iOS app that can perform these functions.