I've done a fair bit more Googling and have come across plenty of people with basically the same problem "ARC worked fine between my LG and Onkyo, until it started working intermittently".

I keep finding new variations on things that will fix it. Latest one was switching the TV from ARC, back to internal speaker, back to ARC. Fixed.

Ten minutes later during more testing, ARC not working again. Switching between ARC/TV speaker didn't fix it.

One of the most frustratingly random bugs I've come across

In good news, it would appear that the LG Magic Remote can also be used to control the amp via IR (at the moment all the amp control is via HDMI/CEC, which won't work when I switch to an optical cable).