Manning n is a coefficient that is measured in the lab when the river is flowing at “normal depth”, meaning your bed slope, water surface slope, and energy slope are all identical.
If there is a big backwater effect, which you might expect to see at a junction with a large river, this assumption breaks down. I think would then expect you manning n to be fudged lower to account for the back water effect.
Maybe first try and calibrate the reach upstream of the backwater in some areas that are approaching normal depth condition. This would be the reach’s “correct” manning value. Then in the area effected by backwater you know it should be somewhere between this and zero.
Hope that helps.