Hi there
Ummm, yeah. Good luck with that one. 
I say this because the "working" WAV files are stored inside the .CPTX file. And I'm unaware of a way to manipulate that file using any application other than Captivate.
My guess here is that the best likely approach would involve saving the modified files to a specific location, then importing them into the project and configuring the desired elements to point to the modified versions. Once you did that, the library should then recognize that the file exists on a hard drive location. And if that works as I think it may, you could then achieve the "round tripping" if you needed to further edit the files.
Cheers... Rick 