And all we know from Secret Wars is that Thor was worthy enough he could no longer lift Thorr's hammer. Whether he became worthy enough to lift his own is never answered, to my knowledge.
But as the timeline was rebooted, the entire thing never happened in the current MU so as far as I know, it has no bearing on the Odinson. Perhaps he was truly worthy in those last moments against the Beyonders, but it doesn't matter because that didn't happen in the current reality. The incursions never happened, so Thor never fought an army of Beyonders and whatever degree of worthiness he regained didnt happen either.