Correct, by doing the 24/96 -> 16/44 > 24/96 route you can seamlesly join the clips back to an apparent 24/96 file but some clips are actually only 16/44 resolution. Easy to do, easy to test if you can hear the difference. I did this to a Linn "Studio Master" 24/96 file with Adobe audition and can not hear where the music was cut & downsampled.
Surprised you might be, maybe also disapointed...
Basically that conversion does not touch the 15 most important bits, and dithering only the last half bit depending on the settings, upconversion basically does nothing but adds the missing 8 zeros to the end and have absolutelly zero effect on the sound quality. This would be the case with 44.1 - 88.2 kHz conversions, recalculation needed for 96 - 44.1 -96 operations generate some artefacts, but apparently they can not be heard.
Like I said, nice exercise, does not cost anything if you have a true hi-rez file to manipulate (be carefull with the naming of files), needs no special test arrangements.