Clemens,
I tested your case with v7p3r0 and with a scalar execution (executable compiled without mpi libraries and parallel processors = 0).
From the second iteration, the hydro solver doesn't converge (NaN values appear). After some investigations (I ran your case in offline mode: T2D first and then SIS with hydrodynamic file from previous T2D computation) I found that you're prescribing no bottom elevations on your liquid boundaries (LIEBOR=2 wall conditions in your *.cli file) that lead to an incompatibility during the resolution of mass conservation over these boundary nodes. If you set LIEBOR=4 (free bottom evolutions), your case runs fine.
I strongly advice you the improve the resolution of your mesh near the river boundary and check the global quality of your mesh (it contains many weird elements, able to trouble the run).
By the way, your sisyphe steering file contains both BEDLOAD and SUSPENSION processes. For bedload computation, you're using Soulsby/Van Rijn formula which already accounts for suspension effects, so you're considering it twice by turning on SUSPENSION too. I advise you to turn off the suspension, or to choice another bedload formula that does not account for suspension effects.
I hope it helps.
Regards,
Laurent