I have accidently deleted my wrk files out of cakewalk. they're still in the E drive in the form of over 12,000 wave data files. How can I return wave data back into Cakewalk intact?

The wrk files are the project files and contain midi data and pointers to the audio files (which are wave files).  I think you will see that the wave files all have computer generated names and can't (as far as I know) be related  back to the original projects (that is, back to the wrk files). 
 
Unless you have backups of the wrk files I think you are out of luck.
 
--Larry