VS 2008 'Synchronizing' File Contents?

I am writing a text editor application which uses an advanced third party text editor. This editor allows the user to set Bookmarks and use Outlining, just like the editor in Visual Studio. The output of my application is a ".script" file, which is basically just a text file. This file is read later by a game, and I can therefore not change anything to the layout of the file. It must be a simple text file.

When the user saves any document, I would like my application to also store the Bookmarks in that document, and the state of any Outlining ranges (collapsed or expanded). The editor allows me to do this by using a special Save feature, which saves the contents of the editor (the text), along with its properties, bookmarks, outline ranges, etc to an XML file. I can also load this XML file back. Now there is one obvious problem: my application should still output its documents as ".script" files, which are just normal text files as said above. Therefore, I cannot use the XML files that also hold the properties/bookmarks etc directly, since the game cannot read those!