So I played around with this a bit last night looking specifically at the header trail and couldn't make it work trying different command line parameters with SOX. I checked the pitch on the resulting clips and it's fine.
Here's another possible piece of the puzzle though: going from 44.1k to 48k the resulting 48k will have more samples for the same time duration. What's probably happening is that although Sonar is recognizing the higher 48k sample rate there's probably a clip parameter under the hood that represents the total sample count and perhaps the 44.1k sample count is still associated with the clip instead of the 48k sample count. This is consistent with the symptom I'm experiencing in which the last 10% or so of the audio is missing in the clip.
Does this spur any more ideas with anyone?
Just to reiterate, if I import one of the underlying wav files into Sonar in a new location there is no problem; Sonar recognizes 100% of the audio in the clip at the correct sample rate. This also supports the idea that the wav files are not the problem, but it's more likely the glue in Sonar that binds the wav files to the Sonar clips.
More ideas anyone?