Originally posted by BiB
No, it won't.
You have to change Portugal to be not a major country.
The easiest way to do this is before you start the game: Copy the GC scenario file (or IGC, or whatever you're playing), and go in and look at the list of eight major countries at the start. Replace Portugal with anyone else (for example, turn China into a major power). Then play your copied scenario instead of the GC, and Portugal can be annexed.
There are detailed instructions on scenario editing available on the two FAQ sites and in the Scenarios forum, I think.
If you want to change it in the middle of a game, you have to edit the save file. This is a little more difficult, because the game keeps track of all kinds of stats on the major powers. So, to de-majorize Portugal and majorize China in their place, you have to not only change the tag, but also change all kinds of other stuff (number of cities, colonies, and trading posts, etc.). Most of this information won't hurt much if you don't fix it, but some can cause the game to crash when you try to reload, so be careful.
There's also all kinds of historical stats that the game keeps track of for the major powers, which you won't have enough information to change correctly--but fortunately, this will only affect the graphs in your ledger and the end-of-game report.
Portugal also didn't take too much time before breaking away again.
The game already allows for countries to be annexed and then later revolt. It happens all the time in the game. So that's no reason to make annexation of Portugal impossible.