From what I understand, we have two systems aiding us in cleaning up in a OEI scenario. There's the landing gear transfer valve and the PTU. Regarding the PTU, again from my understanding, it ensures that the clean up can be done without delay. Also, it provides you with autoslats. However, when it comes to the alternate system, when you put the alternate flaps switch to the down position your LEDs will move to full extend.
From what I gather from the initial post, the question is; can the LEDs be retracted from this position? I think they can. But entirely in a test situation, because you wouldn't have used the alt system unless SYS B was gone. So, my answer will be you can retract them provided you have SYS B pressure and fluid, however not by PTU (A pressure, B fluid).
Hope that helps.