Conformed Files

Two different times I have gone to my music files and found them empty.  All that was left was the .wav files that I had started with. What I did find was the Audition CC had stripped twenty five of my music folders and place all of them in a single music file.  I found them by accident.  I ended up with conformed files.  I don't use conformed files for anything and they are now causing problems.  Right now I have about two hundred music folders with 68.4 GB of data. I am not having a problem with storage on my hard drive.  I am running a 2TB hard drive with it about half filled and 8GB of RAM.   How do I prevent this from happening again?  Did I do it?  Can I turn it off?  In other words, what is my problem?  To me it appears of if Audition CC had a hiccup and this is what came out.

Jim