To re-fit (fuel and ammo), you only need a "friendly" base, as denoted on the Navigation Chart map with the upright anchors. If you're based at Pearl, Midway is good, or Fremantle, Brisbane, Dutch Harbor, and others as the game progresses. To "End Patrol", you need your "Home Base", which is the tilted anchor. If you start in Manila, it will change to Surabaya then to Fremantle, and you may or may not notice the passage of the message in the text box and / or radio messages. I've missed it more than once.
In the stock game, and some of the mods, there is like a two or three day pauses between bases, so you might see that Manila disappears as a base, and two or three days later, Surabaya is now "Home", and when it disappears, it'll be a few days before Fremantle shows as "Home". I do not recall the exact time frames involved, and I also do not know if it's intentional that it happens like that, to simulate the bases actually moving operations, or if it's because of a calendar problem... Some one has probably mentioned the "why" elsewhere in a post on this site...
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