Dear Jean-Phillipe,
your problem looks very interesting! For your case, you can try:
(1) running a 'chained method': that is, providing your previously computed hydrodynamics field to Sisyphe by using the keyword: FICHIER HYDRODYNAMIQUE = 'name of t2d the file' and running Sisyphe as stand-alone. In this case the morphodynamics will be modified at each hydrodynamic time step, but be aware that the flow variables won't be updated as does in the internal coupling way (again, I don't like this approach...).
(2) running the internal coupling and using the following keyword in the Telemac steering file: COUPLING PERIOD FOR SISYPHE. In this way, will have the control to update your morphodynamics as you wish. Probably, a sensitivity analysis will be necessary to see the influence of your results to this parameter.
I hope this helps,
please take us informed
all the best,
Pablo