Sample rate conversion happens all the time. The 96kHz will convert nicely because it is exactly double 48 kHz. People also convert 44.1kHz to 48kHz constantly because 44.1 is the CD standard. Sample rate conversion is a hassle, but not a disaster. I wouldn't think you will have problems with sync drift, especially on the 96kHz track.
I use BIAS Peak for conversions, but just about any audio editor should handle the task.