**Before you start deleting folders, make sure you have a backup of your current configuration.**
This is what I ended up doing to clean up my unused CDAT folders.
I opened the Whistler programming software, connected my scanner to the PC with it turned off until it recognized it as an 'external drive'.
I then individually selected my V-Scanner folders, and viewed the contents to find the folder that was the one with the current configuration I'm using. I then copied the contents (mine was all in CDAT_VS.002, yours may vary) to the Default folder, which in my case had early data that I wasn't currently using. I then checked CDAT_VS.003, which had nothing current in it either, but was an copy of an earlier configuration I was no longer interested in, so I deleted it. After copying the contents I was using to the main CDAT folder, I then copied those contents to an extra CDAT folder to save as a backup. If you travel with your scanner you can use the CDAT folders for different configurations. In my case, my TRX-2 stays in the shack so I just copied it into an extra CDAT folder for a backup.
I then clicked on the Scanner/SDCard tab, and selected Optimize Scanner Memory/SDCard. This takes awhile, as it optimizes it and sends it back to the SD Card in the scanner.
When you're done, select File, Open V Scanner Folder, and then select the folder you use for your current data, and check the box at the bottom to set the selected V Scanner Folder to be used at Startup. To finish, I again copied the configuration to the Scanner/SD Card one final time.
After that was finished, I deleted the CDAT folders I was no longer using.
Hope this helps.