Spain's comeback

So far, I haven't seen an invasion force originating from a Settlement and I'd be surprised to see that happen.

However, you can aggravate a single city by capturing several of their nation's ships going to or leaving from that port. If it takes too long, you can raise their anger by pelting their fortress with shots on the world map. To do so, hit "Space" to shoot at their fortress when you are close to the city.

Soon the port's fortress will take shots at you, meaning that the city has started treating you as an enemy, allowing you to attack it. Once you capture the city and your troops sufficiently outnumber the remaining defenders you may install a Spanish viceroy as the new Governor, giving Spain a new foothold in the colonies.

Note that, both, the ship blockade and the bombardment, reduce the wealth of the city.

I haven't played in a while, but I ran into this exact thing a long time ago. My solution was to reinstate the Spanish Empire by conquering another port (I was fighting for the English, and we were also at war with the French at this point) that was French and reinstating a Spanish Governor, because it gave me the option of what country's banner I wanted to install. Using this method, I was able to reinstate the Spanish Empire, but because I was conquering cities for the Spanish, I quickly gained reputation there and ended up becoming a Count or something...

I know the newer version of Pirates! now has settlements, which I have seen can spontaneously generate a colony of any nationality, so I would think that given a weak enough port, the settlement could in theory capture the port, thus returning a nearly extinct empire to the map. I've not yet seen that exact thing happen, but I would only assume it's possible given I've received news that cities have been captured (ie changed flags) without my intervention at times.