Saying 'should i convert them to xml or something' is a bit nebulous.
I guess what you really asking is: Should I rewrite my application entirely in Adobe technologies or Can I/Should I integrate it with my existing PHP code.
I would recommend you expose the existing PHP functionality as RESTful web services and redo the user interface in Adobe AIR. That way you can leverage the existing site to make the desktop application. There is a ton of information of building applications like this, just research REST, SOA (service oriented architecture), SAAS (Software as a Service).
Adobe AIR/Flex is fine, especially if you want it to work on multiple operating systems, but the Application won't necessary have the looking and feel of its host desktop environment.