After about 40-50 days, you should be ending patrol. While the SH4 game doesn't do a very good job of crew stress, anything over 50 days in real life would be pushing it. FotRSU will give you radio messages for certain circumstances, such as "Cavite Naval Base is under attack and being bombed", "Cavite Naval Base is no longer in service. Re-fits can be performed at the Manila docks"... "Marivelles has been established as the only re-fit location in the Manila area" (or however they are worded). You should also have a message such as "All Asiatic Submarines are hereby ordered to the Malay Barrier at the end of their current patrols", so nothing that says "Surabaya is your new base". You have to look at the anchor symbols of the Allied Naval Bases for one that is slanting, which is your new "Home Port" - for now. As of now, you'll go from Manila to Surabaya to Fremantle only. At some point in the future, and add-in mod might be available to other routing, but that will be a while, if it happens.
As for the ship with the white flag, and one that appeared to be possibly neutral, be very careful of them. The Germans, and then the Japanese employed "Auxilary Cruisers", which were ships disguised as merchants, sometimes flying flags of neutrality, but having their decks bristling with guns, and sometimes a scout plane. Cheeky tricksters... The idea was to lure a submarine in close, which would then surface for battle stations deckgun, and find to their horror, that the "merchant" was actually a warship.
