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I bet the timeline Thanos left from and thus became a branch ("the universe without Thanos") was wiped out five minutes after he left by the TVA. He did not have to be wiped from the 'sacred timeline' after that since he was definitively destroyed by the Avengers about an hour after he arrived in the future, along with all his minions. Aha! I just realized why not! Everything that is wiped out, is not really wiped out - it is sent to "Beyond the end of time", let's call it Limbo, to be destroyed by Alioth. I think He-Who-Remains was not confident that even Alioth could defeat Thanos and his minions, and rather than risking it, leave it to the Avengers.