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NextDownID = -1 but not outlet

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I've built my network; set my flow direction; asigned HydroIDs to my pts, net_junctions & lines; run the From/To nodes for the lines; and lastly NextDownID for the lines. I have 57 line segments with -1 as the NextDownID. I only have one true outlet for the network.

I have no disconnections in the network when I run a trace. All of the From/To Node fields are populated and have the correct HydroID for the next downstream segment. The segments with the -1's are not endpoints but a segment within the total stream length. Unfortunately, this is a fairly large network and takes four hours to run the NextDownID, so it's not an easy test for fixes unless I break out a portion of the network and test on it. I have disconnected the network, stripped out all Hydro/JunctionIDs, and rerun from scratch to see if I missed a step.

Any suggestions are appreciated!

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