This is strange. It worked for a while, so I shut down and re-assembled the unit and gave it to my brother for Christmas.
When we plugged it in to try it out, the remote did not work.
I thought that maybe the IR connector or wires were loose or damaged by my reassembly, so I put the android eMMC back in and booted that, only to find that the remote does work there... so it is a software and not a hardware problem.
I switched back to the LibreELEC eMMC, and verified:
/storage/.config/rc_maps.cfg
still contains
* * pine64
I had to change this to:
* * pine64.toml
Now the remote is working again.