What is the proper way to convert a pair of three-way (SPDT) switches into a single two-way (SPST) switch?
Use a smart switch capable of supporting a wireless remote, so when the AHJ flags you for failing to have requisite switches, you can just glue a wireless to the wall.  

Black and white are currently travelers.  The red is switched-hot, which is awesome because it'll stay that.  

Re-task black to be always-hot, by moving it in box A to the always-hot bundle on the wire nut.  

Re-task white to be neutral, by moving it in box A to the same bundle of all-whites that the lamp uses.

At this point there are no wires on the upper switch in the duplex switch. Convert to a single switch. 

Now install the smart switch in box "B".