Do you have a link to the pattern??? That might help a bit more.
I think sometimes when using a pattern which is written for double pointed needles, it will ask you to re-distribute the stitches by slipping back and forth between needles until you have the correct configuration to continue on with the next instructions. Obviously things are different when you use the magic loop method and you may not have to slip anything at all.
Usually when I've used magic loop for a sock, the last heel turn row will be a right side row and from then the next instruction is to start picking up stitches along the heel flap.
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