yeah for now I've just made sure I set the temperature lower on my custom maps. Most multiplayer maps seem to be set on 30C, which doesn't create a problem. For some reason mine was set on 42C which apparently is too hot to operate a F16. I think this is a bug though and needs to be raised more, but we'll see.
I think the longer this warning is on, the more damage that can be done. I've had it damage my avionics and I think the FCS a few times already. But no problems once I set the temp of the map lower.