Project hang: 1 second on 3 seconds donut of death RH9

My large project has become unusable after deleting cpd file.

My cpd file was becoming quite large (15MB) and my project was slowing down, so I deleted the CPD file and reopened RH9 to regenerate the file. This normally takes about 60-90 minutes, but this time I let it run overnight. Now it is acting like it is still working on this update. When I open the project, I can work fine for about 30 seconds. Then I get an alternating cursor arrow and wait cursor (donut of death): one second for arrow and 3 seconds for donut. This makes it impossible to work.

The CPD file is about 3MB now.

The status bar alternates between "Ready" and "Loading topic list..."

This is a large-ish project with hundreds of topics, images, and snippets, but it has worked fine up until now.

Does anybody have any ideas?