The meaning of the Fool's prophecy in Act 3, Scene 2 has been debated. It is cryptic. There are even some scholars who suppose that Shakespeare did not write it or that it has been misprinted. There is no proof of this other than some inconsistencies in early manuscripts of the play. In either case, it is in the play, so what could it mean?
In general, the Fool is saying that when things will be as bad as they are now (in that moment with Fool, Kent, and Lear), Albion (Britain) will be in chaos. Albion and the reference to Merlin recall the tale of King Arthur and his supposed return. Arthur will return when Britain is in dire need; he will come and restore Britain to new glory, a utopia. The time for Merlin's prophecy will be when "slanders do not live in tongues" and "bawds and whores do churches build," two phenomena that, while they sound strangely promising, are quite bizarre.
The Fool is a counter to Lear. When Lear is behaving insanely, the Fool gives satiric but genuine advice. When Lear's "wits begin to turn" in this scene and he humanely asks the Fool if he is cold, the Fool must be counter (cryptic) to Lear's temporary logical statements. Therefore, the Fool's prophecy is not clear, like Lear's previous and subsequent mad behavior. The lack of lucidity of the prophecy reflects the chaos of Lear's mind and the kingdom at that present state. The Fool's sarcasm and confusing descriptions within the prophecy (i.e., "when bawds and whores do churches build") also symbolize this chaos.
Also remember that the Fool's prophecy, as bizarre and unclear as it is, describes Albion (Britain) in chaos. Then he says Merlin will make this prophecy in the future. So, the Fool is making a prophecy of a prophecy, living in Britain at a chaotic time and making a prediction of a time when Britain will be in a chaotic time (at which time, Merline will make his similar prophecy). Since it is in chaos now (the Fool's time), the prediction is bleak in that Britain will be in chaos for some time.