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It is a little tough to see what is going on even with the attachment, but it is an interesting problem. It looks like at low flow, the junction is downstream of the bridges, but at high flow the bridges are essentially inside of the junction? Where you have drawn the two question marks, do you think this flow is parallel to the tributary and still entering the Ohio, or is this flow already in the Ohio and is parallel to the Ohio?
In either case, I can't imagine that "run our downstream cross sections parallel to the contours and never reach the max level" is a good idea. I would be more inclined to either dogleg the trib cross sections lines to the right to capture the high ground (if this is trib flow) or extend the Ohio cross sections over the roadway (if this is Ohio flow).
In general, you want the flow to stay perpendicular to the cross section lines, even if you have to bend the cross sections to do that. If the flow direction changes radically between low flow and high flow, RAS may not be able to capture both behaviors with the same data set. Or, to model it with a single model, might require a more ad hoc approach.
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