I haven't tested yet, but I wonder if Quattro would load a previously saved CD layout that was built using 44.1 files with 96k files swapped out in the same folder. Hmmm.. I'll need to check that later. If that works, I'd at least save the 96k bounces with the project just in case.
are you upsampling the source file in PT? running the source session in 24/96?
and are you catching through a separate track recording in PT and then exporting to a flat file? or bouncing directly to a flat file?
Any SRC before going to DSP Quattro? and finally, what are you using in DSP Quattro for dithering down to 16?
Stefano actually just released a new version today,... Exciting times are ahead.
Note: I do not use plug-ins and am gun-shy about sample rate conversion.