I think you might be over complicating this. If you want a subset of the recordings in SONAR and don't want to backup the files I think you can do it all inside SONAR without any external apps.
- Import the original wave files choosing NOT to copy the wave files. This will reference the original files.
- trim the clips as desired in SONAR
- select all the clips and choose apply trimming to keep only the trimmed data
- File save as and choose to save a bundle file. This will save a bundle of only the trimmed audio
- Reopen bundle to a new per project audio file and let it create a file per clip. You now have clean wave files for exactly what was trimmed
- delete the original source wave files once you are sure you have what you need