On Wed, May 14, 2014 at 11:31 PM, Arun Persaud <apersaud@lbl.gov> wrote:
had another look and org-export-filter-final-output-functions is the
wrong function to use. ...

So, I ended up solving my problem, via an alternative route. The code is here:

https://github.com/chrispoole643/org-gtd/blob/dcfe7122fa496de51a8de3a8f02184bc7aec05b9/org-gtd.el#L143

Essentially, the icalendar function that combines the agendas and exports stuff just calls a function that happens to accept a restricted list of items to export. So, I use this function directly, but first I look through my agenda files and mark where the scheduled tasks are. I then pass these as the restricted list, and all works well :)

Thanks for the help,
Chris