Hmm: I don't think it can be done that way. You can't search for hypelinks and text doesn't have any collections that help. If you watch what happens in the UI as you move the insertion point cursor through the source text, you'll see that contrary to what I was thinking, there is no marker in the text, so it must be operating in reverse, oberving the text ranges involved and highlighting as you work.
So, that suggests that your script is going to have to work in a similar fashion.
Have I pointed you enough in the right direction or do you need some more help? I think if you do need more help, I need some more specific information -- how do you know which cross reference you want to change? Or are you really looking to change all the cross references that use a particular format to use a different one? Or perhaps you want to redefine an existing format?
Dave