Altium PCB layout net error
In your PCB Doc go to Design tab up in the top toolbar, then Netlist, then Clear all nets. Then re-import changes from schematics, and it will re-assign all the nets, and re-establish traces which do not 'collide' anymore. 

Be aware that this may bust the net labels given to polygon pours and vias which are 'free' in the document. I guess just in case, copy the PCBdoc file somewhere as a backup before doing this.