As long as both plugs are in or just ploug 0one plug in, aafter wrapping a few wraps of electrical tape around the other cords plug to cover the prongs, there shold not really be any reason to have to unplug it. While it may not be wired correctly, at least it will not present a shock hazzard as a lot of folks have reported, and it certainly should not start a fire.......
Just pick one light assembly to utilze, , identify cord for that light, and wrap other plug on other cord up with tape and bump on until they get the fix to you, no sense loosing anyhting with the screwup...
From what I seen and heard, they (current) is offering folks a retro kit to include a dual timer, instructions to modify existing wire and needed insulated tape or cap etc, and a free t shirt or hat or something along those line........Seems its a quick fix according to some, snip one wire and cap both ends with insulated cap.......it appears they fed both lights ballasts independantly as well as with a jumper between the two as well so they get feedback through the ballast if one is off and it keeps the lights from being used correctly with a timer.
I would certaily expect a replacement whatever upfront first, and use the AP until that time with 1/2 the lights being utilized.