If a player EVAs from the Primary Command Pod and enters a Chair connected to the craft on the other side of a set of Docking Ports, which has a Command Chip, but does not disconnect the Dock before entering the Chair, after undocking the Command Chip will not control the craft, and on additional EVA the player cannot re-enter the chair.
On the same craft, if instead the player EVAs, tether's to the docked Chair/Chip craft but does not enter the chair, undocks, then enters the chair and controls from the Command Chip, then the Command Chip will control the craft as expected.
@sflanker thank you!