This should be fixed on the next patch, so we could get lucky. Actually, the server [b]is[b] capable of graphics, but it does not have a monitor

Dominions2 will not load unless you have the graphics (X) server installed, even if you intend never to use it. But it is unconfigured, and starting it would probably kill the poor thing under it's current load.
As for stop->trans->make computer controlled->trans->restart, that just might work. But it is,,as you say, quite bothersome. Worse, it sounds risky. I might do it anyhow, since the 18-hours schedule is a bit sad...
Why does every game have at least one AWOL? :'-(