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In the booksEdit
Every king of the Targaryen dynasty held the title "Lord of the Seven Kingdoms", even dating back to Aegon I himself - despite the fact that Aegon I never managed to conquer Dorne, which only joined the Targaryen realm through peaceful marriage-alliance fully two centuries after the War of Conquest (about one century before the War of the Five Kings).
This is not because the Riverlands were upgraded in some fashion to be considered the "seventh" kingdom: the "Seven Kingdoms" was a geographical term for centuries before the conquest, and Dorne was always one of the "seven".
The explanation is that when Aegon I began his conquest of Westeros, he unilaterally declared himself king and lord of all of the Seven Kingdoms, before proceeding to actually conquer kingdoms such as the Reach or the Westerlands. Aegon's armies were repulsed from Dorne due to guerrilla warfare - but he never stopped claiming the title. Subsequent Targaryen kings continued to use the title "Lord of the Seven Kingdoms" as a tacit declaration that they still laid claim to Dorne and intended to conquer it eventually. A century and a half later, King Daeron I even managed to briefly conquer Dorne, but the occupation was thrown off and it remained independent for another half century.
This is loosely comparable to how some real-life medieval monarchies continued to claim titles that they no longer possessed de facto, i.e. how the kings of England might style themselves as "lord of Ireland" or "lord of Wales" even at times when most of Ireland and Wales were ruled by functionally independent princes and kings. The oddity of the early Targaryen kings laying claim to Dorne is that unlike English kings who lost territory in Ireland but still claimed it, the Targaryens never even conquered Dorne in the first place, nor did they have any other real legal claim to it.