I had a similar problem earlier, but I never figured out how to fix it. My PCB was fine, then I needed to switch a few lines around, and move some chips around. Moving was a nightmare, some traces connected to other traces. I did a lot of deleting and rerouting. I finally got it down to two nets. When I fix both, then when I run DRC I get a Clearance violation where the traces connected to net JP15-B are now JP13-B. JP13-B and JP15-B are the two lines I needed to switch. I have I keep fixing, they keep getting screwed up. I have updated PCB from schematic, with and without re-inking, but no change. How can I fix this?
Nevermind, I found the problem. Nets JP13 and JP15 were connected by a short trace, which usually was obscured by a trace on the other layer. Once I deleted that, everything went together. Oh the joys of moving parts in KiCad 
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