I believe the assets file related to Gobbler info, and possibly other "assets" now. Not sure what you mean about the wave files. You can rename them inside of Sonar but that bears little resemblance to their external name, but never has AFAIK.
The best way to manage wave files is from within the project or using the CWAF tool that comes with Sonar. Managing them outside of Sonar is possible but asking for trouble unless you are 100% confident in what you are doing.