You can't convert a PDF file to XML and back without loosing information. To manipulate you need a tool that operates on PDF files. This can be Acrobat, one of the PDF libraries, free tools, etc. Mostly this depends on distribution cost (Acrobat is expensive for many users, cheap for a single user) and PDF file version. Free tools usually only handle the early file versions without encryption, digital right management, content encoding, compression, etc.