I have tried changing the "apply all Inverts" back to pre 2006 defaults however I still get the same problem. I deleted the weir that was seemingly causing the problem however this just changed the location where the hydrograph suddenly drops away. The problem is now occuring at a 1d/2d interface. The 1 and 3 hour event runs fine as the peak flow is only 80m3/s. However once the flow reaches 100m3/s the hydrograph drops to 0. This doesn't occur at any other location of the model. The output hydrograph has NaN where the error occurs. It seems like it is going unstable but continues to run anyway.
The main difference is I have a lateral channel section coming in. The two incoming channels go from 1d to 2d and then back to 1d for the downstream channel. I have attached a diagram illustrating this. The diagram also shows no flow in the 1d channel (probably to do with the NaN) however it is still spilling out into the 2d.
Do you have any ideas of what is causing this? Model_diagram.pdf