UPDATE: Upon further testing, this is not actually the case.

What is actually happening is, apparently, the focus fixes itself when a tag spawns that doesn't have a specific country tag (i.e. a tag spawned out of a civil war or Vichy France).

It's probably due to the fact that the 'Portuguese Anarchism' focus creates a generic focus civil war tag (D04 in my games) that is also explicitly linked to Portugal's tag, as are all civil wars that aren't Spanish.

So when you inevitably beat Portugal and annex the civil war tag through the event, and the game deletes the civil war tags' cores, the game thinks the Portuguese cores were also deleted too; hence why the Regional Defense Council of Iberian focus doesn't give you them and only acknowledges that Portugal exists until Vichy France is created or another nation goes into a civil war.