I had a similar problem five or more years ago on my R27. Nova Kool tech support is very helpful. They felt sure I was not getting full voltage at the refer itself. As I recall, the Nova Kools have a low voltage cutout to protect your batteries from full discharge. So if voltage drops sufficiently at the unit (to 10.6, I think), it will shut down entirely. It will come back on when voltage rises (to 11.7 or so, but I’m not sure on the exact cut out and cut in levels).
In my case, I pulled the refer and seemed to have adequate voltage there. Even so, it would cut out after being underway for awhile and it seemed somewhat arbitrary for when and why it would come back on. At the time, I was parading at night during the holiday season in Portland, and the water can get pretty lumpy when the flow is fast under the bridges and the boats are kicking up a lot of wake between the downtown sea walls. As it turned out, my problem was the connection at the breaker (which was not all that easy to access on that model of R27). When I pulled the panel out enough to get a good look at the breaker, the connection at the breaker breaker was toasted. My guess is that the wire crimp to the connector was bad and the bouncing around at night underway was breaking or even shorting out the connection in some way.
After finding that, I cut off the bad bit of wire, crimped on a new connector, tested the voltage and resistance and all looked good. The breaker seemed to work fine, but I replaced it anyway. Never had another issue with the Nova Kool or the breaker after that.
If you have a low voltage issue, that might explain why the light comes on, and then later goes off. You maybe getting enough voltage at times for the unit to restart and have a light on, but the voltage isn’t consistent long enough for the refer to cool and stay on. That suggests the need to trace the wire and all connections, both at the unit and the breaker. And again, don’t hesitate to call NovaKool. I think you’ll find them helpful, whether you are in or out of warranty.
Good luck!
Gini