net connections that won't go away

I have a circuit from which I *removed* some wires, but when I create a netlist file, the connections (nets) made by the *removed* wires are included in the netlist file. I don't understand why that is happening. As far as I can tell I have removed those connections. Maybe something is cacheing the connections, but I cannot figure out where.

I am using KiCad 4.0.7+dfsg1-1ubuntu2 under Ubuntu 18.04

The project is on GitHub: https://github.com/RobertPHeller/RPi-RRCircuits/tree/master/ESP32-MultiFunction, specifically the Vdd (pin 6) of U11 and U12 in the Buttons4LEDS4.sch file.