Hmm, are we talking about the QuDrive or USB streaming? Yes, the QuDrive takes WAV files and for QuDrive multitrack playback your project needs to be resampled into 18 individual 48kHz mono files. QuDrive can not open project files from any DAW.
If you’re talking about USB streaming so the Qu acts as a kind of Soundcard, resampling requirement depends on what your DAW is willing to do.
If ProTools supports runtime resampling (don’t know) I see no reason why you shouldn’t be able to open a 44.1kHz project and playback through the Qu at 48kHz. However, runtime resampling of many tracks may be a performance issue.