It was never the flag of the legitimate (well...) Second Republic, and it was established that Poland didn't take legal continuity from the Government-in-Exile.
As for the government in 1989 - the people agreed and established that the 1989 Sejm was legitimate.
Alas, that did nto come to pass because Roundtable Poland was spawned at Magdalenka and elsewhere behind the scenes as a collusion of atheist commies and atheist KOR-ites .
How strange - Macierewicz was in the KOR, and Lech Kaczynski took part in the Magdalenka talks. Aren't they your PiS heroes? In fact, there's quite a bizarre episode in the KOR history - Kuron and Michnik got themselves arrested at one point after high level talks between the Poles and Soviets, but Macierewicz strangely wasn't arrested. Why?