All GM examples I've seen on the net the yellow phase wire is always in the centre of line both on the hall sensors and the phase wires.
Green pulls in one direction and Blue the other direction so yellow is the follower to either direction.
So My suggestion is to change blue and green on the phase and on the halls and leave yellow connected to yellow.
The question related to the Magic Pie, and mine is wired like this:
If you click the image to enlarge it, the colours of the hall sensor wires are more obvious.
(I did have to highlight the yellow one because it was a bit camera shy)This is why I originally suggested swapping the Green and Yellow leads:
Have you tried connecting the Reverse connection to ground (0V) on the controller? This may select reverse if it's still enabled on the Pie's controller.
If you're going to swap phase wires instead, I would start by swapping the green and yellow phase wires first, but you will also need to swap the green and yellow hall sensor wires as well!
I gave the same advice a couple of months ago, following an email asking how to reverse the rotation on one of the Magic Pie's fitted to this hybrid car project:
We went for swaPping the winding and hall sensor wires. It worked. Our problem has been solved. Thanks for your help.
So I therefore assumed my suggestion to transpose the Green and Yellow leads was correct.
Alan