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At worst I suspect you may only need to recreate the folders. Try creating a new folder with EXACTLY the same name as a missing one. It might just start showing the files as well and gradually the links should repair.
I've experienced a few folders go missing but not the whole lot.
It might help to know what prompted you to delete the CPD in the first place.
I deleted the CPD file because I got the message "CPD file is corrupted and cannot be opened." I've been to your website before so I reread your instructions for opening Robohelp projects. I deleted it previously and it rebuilt fine. This time was not the case, so I reverted to a previous version of my help and compacted the CPD using the Jet Compact Utility. This is fine at the moment but I'm afraid this problem will reoccur.
Try occasionally compiling a CHM even if that is not your output. That updates the HHP file and might help. You could take a copy of your project now and try it using the copy.