Resolved, the problem was I should not have used find/replace. I thought I had done that before.
Real fix is to load the project as normal and when it complains about a missing file, redirect it to the .ogg version and it will be smart about the rest of them, too. Only, it will ask this once per directory (for example, the 'impulses' folder created by ReaVerb).
Sweet!
My demo projects and jam recording files folder is so much smaller now.