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The Covenant would have worked out the coordinates of Halo the same way Cortana did. Remember that the PoA's seemingly "random jump" was actually a plotted course from Cortana. As the Covenant Fleet were pursuing the Autumnthey would have realised that their trajectory would lead them on an intercept course with one of the coordinates they had discerned from the rock on Cote d'Azure. So, yes they were following the Autumn initially, before realising where they would be and then bet them to it. At least that's how I would reason it.