For Projects that you have finished, you can safely Delete the .CFA and .PEK files. If you are working on a Project, and Delete those, they will be regenerated, if you Open that Project. If so, be patient while all Audio files are Conformed and the .PEK files are generated.
Hunt; thanks again, but does that mean everything in the media cache file
when your done with the project or just .CFA AND PEK files in that folder?
This can depend a bit. If you have done any Rendering, those Render files can be safely eliminated. As mentioned above, the .CFA's and PEK files can also be eliminated (will be regenerated, if needed).
For housekeeping, I place all Scratch Disk files in the Project's folder hierarchy. This keeps everything together and below the Project's root folder. When I am done, I will just Delete everything in that Project. In my case, ALL Imported Assets are ONLY copies. I never work with originals, which are safely stored elsewhere. Basically, one click takes care of the cleanup.
If I am not sure that I am done forever with the Project, I will first use the Archiver (Project Manager in PrPro), and locate the "archived" Project on an external HDD for storage. I will archive ALL aspects, except for the Render files, including the .CFA's and .PEK's, just to save time, should I need to revisit that Project.
There are other files, that are possibly in the Project's root folder, such as when you Burn to Folder. You will then have the VIDEO_TS folder, with the necessary DVD-Video files. Once you have successfully burned that folder to DVD-Video, the VIDEO_TS (and all files), can safely be Deleted.
Hope that this helps,
PS - UNTIL I am 100% certain, that I am done, I do not Move, Rename or Delete anything. When done, I often use the above mentioned Archiver, and then do major clean up.