First some background...
We have a custom piece of software that requires PDF files to auto generate web pages. These PDF files are pretty typical, the only special thing about these is that hey have proprietary programming codes added to the comments/annotations that instructs the 3rd party software on how to transform certain things. To any tool capable of opening PDF files it just sees a bunch of plain text annotations/comments no different from any other PDF.
Because we need to create hundreds of these pages and manage them in a source control system we are considering working directly with the PDF file. Previously we have had an .ai file that is exported to .pdf then the PDF is "marked up" (has the special codes added to the comments) finally the file is commited to source control. This means we have two files to manage keeping in sync.
This is why we are investigating using he Illustrator option "Preserve Illustrator Editing Capabilities" so we can work directly in the PDF files and avoid the storage/management of a .ai file as well as .pdf file.
Our current graphic designer claims this option limits his ability to edit the file (despite the obvious message to the contrary in Illustrator) his predecesor claimed it worked fine.
As I am just a programmer who is having to manage this graphic design process I am wondering if in fact the option works and if anybody knows of any "gotchas" with it.