The bloated CPD may very well be causing a slow project. You can safely delete the CPD files (RoboHelp will create a new one when you reopen the project.)
If you want to be sure, make a backup of the CPD files just as a precaution.
Just to add to what Willam has said, can you tell us what you mean by "cloned". I ask because it is not normal to have two of any project file in the same directory. Whilst deleting the CPD files may solve this issue, I wonder if you'll get other issues further down the line.
"Cloned" isn't a very good description... I created the new project by copying the entire DB of the old source project, then renamed the new project.
Thanks for the help… I had copied an entire project—I was leary of just copying parts.
Deleting the .cpd files fixed all of my problems it seems…