Hi Jason,
sediment discharge QS is calculated in e.g. bedload_meyer.f this is printed in the results file as a capacity. If the sediment is limited (rigid bed, multiple sediments) the sediment fluxes are changed and limited to their availability. This is done in positive_depth_nerd.f (e.g.) So far as I understood is in case of a dirictlet boundary condition for the bed height, the sediment discharge is also changed in this subroutine in the subroutine FLBOR.
I have 2 ideas why your calculations don't fit to telemac results: The fluxes can be given by mass or by volumes with pores or volumes without pores. So if your factor is around 2650 or 1500 it could be this. FUrthermore, the shear stress in gaia is calculated from skin friction by default and not from the friction set in telemac. I can not guess how much this would change your values, but probably not so much.
Best regards,
Rebekka