If you can get the custom fields to show up in a report that will be the easiest. I don't know if that is possible or not.

Beyond that, there is an AppleScript dictionary.  Open QuickBooks in Apple's ScriptEditor (in the Utilities folder) and you'll see the commands.

But I suspect the command you'll wnant to use is executeqbxml.  

And that will then require QBXML commands to pull invoices and then whether or not that includes custom data I don't know.