I opened a case and TAC changed the number of processors on the server settings, but this still didn't resolve the issue.
I resolved the issue by performing the below. If you have a similar issue, most likely this same process will fix it. The APs that were not showing up were all AP61s.
1. Delete APs from Airwave
2. Let Airwave find the APs again by polling controller and place them in their folders
3. Enter the CLI for the Airwave server and restart the Airwave database
4. Go back to Airwave and the APs will be available to deploy onto the floor plan/s