My homebridge randomly restarted, and upon restart, its log showed Indigo connection error: ERRCONNREFUSED. This doesn't usually happen, but once happened, homebridge would log "created 0 accessories", and thus HomeKit will delete everything from homebridge, and in turn all room configurations etc get lost.
Suggest in the function of sending "devices.json" request, upong asyncError, instead of only logging the error, but also try re-send the request, and/or (upon repeated failing) restart homebridge or homebridge-indigo.