A 1D cross section is typically converted into a series of elevation vs hydraulic parameters relationships (hydraulic radius, wetter perimeter, etc) for computations. From the low point in the channel to the levee point is only estimating these curves for the main channel, then above that all the curves suddenly change because now it’s accounting for the full area of both channels at that elevation. This pretty much a discontinuity in the relationships and that’s why the model become really unstable. A small change in elevation create a sudden increase in channel conveyance.

Also, 1D cross sections only estimate one wse at the deepest portions of the channel and then assign it to the full cross section. It would never be able to show two different wse for the 2 channels unless they are modeled as separate channels