As far as I know, they would move over to Allied control. No “reversion to neutrality” rule has been mentioned.
However, a good number of the neutrals in this version of the game that were neutral territories in previous versions (Spain?, Switzerland, Sweden, Portugal, and most of South America for instance) have no IPC value, and therefore they probably will not be invaded. So long as Spain, Switzerland, and Sweden have no IPC value, there really aren’t many good reasons to invade them, because you can’t build an IC on them (which with Spain might be nice for Germany) and they aren’t really in the way of you getting anywhere you need to go. Spain is on the end of the European continent (only reason might be to get at Gibraltar easier), though it may have an IPC mark covered up by that Italian tank. Portugal is even more of a dead end than Spain. Switzerland (assuming a territory setup similar to AA50) is between Italy and Germany, but tanks and mech would have to blitz through to get from one to the other anyway and should still be able to blitz around through the adjacent territory (which used to be Balkans in AA50), so taking Switzerland shouldn’t really accomplish anything. Norway and Finland are connected without having to go through Sweden. With these considerations plus a (hopefully) large infantry spawn should make invading these neutrals out of the question as it would be a waste of resources. No one is going to want to invade Switzerland and fight a bunch of infantry just to have the territory unless they’re already winning anyway. These neutrals are also going to be “true” neutrals that will not be on either side of the playing field.
Other new neutrals like in the Middle East and Brazil were NOT neutral in AA50 and previous versions, because they WERE invaded/occupied/whatever in the actual war. Most, if not all, of these will be pro-Axis or pro-Allies neutrals which is suggestive anyway. So I don’t think there will be too many problems with historical playout. The cool thing is that it at least gives you the option to invade them if you want to put an airbase or naval base in Sweden for example, which is exactly what A&A is all about. 8-)