I don't think it sounds like the bundle files are corrupt. Back them all, *.CWB and *.BUN to CD to ensure you don't lose them.
Try firstly just renaming AUD.INI to AUD.INI.OLD - this will make Sonar re-create the file the next time you run it.
If that doesn't work, reinstall over the top of Sonar, (leaving all directories in place).
If that doesn't work, back everything up, delete and remove any reference to Cakewalk, Sonar, Twelve Tone System, CWPA, CWP, CWB, BUN and WRK that you can find in the filesystem and in the registry.
Truly - this sounds like a config issue, not a corrupted .BUN file problem.
Also - can't remember if anyone mentioned this or not. In Sonar if you hold down the SHIFT key at the same time as you try and open your files, it will ask for confirmation of each and every plug-in. If you say NOT TO ALL, the file should probably open and you will be able to save it out as a different name. (Make sure you save as a different name or you will lose any plug-ins and settings that you may have used.
Ciao,
Q.