Hi Gareth,
In my experience, using two different BC files Telemac2D and Sisyphe, is often necessary. For example, in hydrodynamics you need to define water level and velocities (ie LIHBOR, LIUBOR, LIVBOR: 5 6 6), whereas the respective LIEBOR, LICBOR, LIQBOR in SISYPHE have no prescription, thus are left free (4 4 4). However, as Michiel pointed out, it is pretty much critical to prescribe zero bed evolution at the boundaries (EBOR) so as to ensure your hydrodynamic boundary conditions remain within the defined scope.
In your case, having too much evolution at the boundary nodes is messing with your computation, hence fixing EBOR would do good. However you still need investigate the cause of the large evolution, which, given its extent, will inevitably cause problems downstream of the boundary.
Best Regards,
Costas