Here’s a workaround offered by Antares support (in cooperation with Cakewalk).
1. Do a “save-as” of a given project.
2. In the new file, copy and paste any tracks that AutoTune won’t pitch-track to new audio tracks at the front of the project. (I found that AutoTune wouldn’t function in my project with any audio beyond 1 minute, 50 seconds.)
3. Apply pitch changes, and using Sonar’s standard features, export the modified tracks as high-quality wave files to a suitable location (desktop, for example).
4. Import these wave files into the original project in the required locations. Delete the “save-as” version of the project if you’re short on computing power.