Assuming that Daniels wasn't lying, and the Xindi crisis was never meant to happen, that would de facto mean that the prime timeline was overwritten by ENT's season 3, no?I'd be the last person to give These are the Voyages... credence (especially what seems to have gone down in history as the final voyage of the NX-01).
However in 2371, Riker & Troi are able to summon up a holodeck program and overhear Archer talking to T'Pol about how Shran helped him get onboard the Xindi weapon.
Now we can debate how those TNG characters look nothing like they did during The Pegasus, but the intention is clear. Enterprise as seen for 4 years, was intended to have happened in the Prime timeline's past. There were obviously some changes for Daniels but since every decision a person makes does so, maybe all Temporal Agents operate outside the timeline and act as the self appointed authority on which alternate realities to allow to exist and which not to.
BTW, TATV? That is one episode for which we can say with utmost certainty that it happened in some obscure, never before seen alternate reality in which Riker and Troi at some point contracted some contagious form of progeria, Thomas Riker served aboard Enterprise, science uniforms weren't blue but turquoise and Starfleet officers were all suicidal.