With some limitations (for the DC and Nyquist components), the Hilbert transform is nothing more than a 90 degree phase shift.
I have not found a Hilbert transform that works directly on waveforms, just on 1D arrays. Since it will not change any other waveform attributes, you might want to do the Hilbert transform before building the waveform or use the attached code (image).
It seems to work with any size waveforms I tried.
If this does not solve your problem, please describe in more detail how you are transforming, maybe attach some sample code.