Ok, I restarted my game before the refit and getting the same mission. I motored over to Brisbane...friggin haul. I could not end patrol but I could refit. Now, on the way over PAC news said the Japanese were operating off Darwin. So like any good commander, I headed that way to patrol. While enroute, Java was lost to the Japanese. I suspect I will get a message very soon to start using Femantle or Brisbane. Perhaps for lack of different missions in between patrolling and losing your base this is all the developers did. Therefore, I suspect you get the repeat until such a time in the simulated history you lose your port. Now, lets see if I get the message after I report in my sinkings and that I'm out of fish.
I think you have to call the shots sometimes like the commanders did. I know the commander of Wahoo demanded he go back to the Sea of Japan because his first trip was fruitless with dud torps. He was granted this request and if not he probably would have done it anyway. It was Wahoo's last patrol.
So I hunt around Darwin and see what happens