Believe it or not, years ago I designed a conveyor that did nearly the same thing. I used permanent magnet rollers (for which I learned the VERY HARD way that you MUST use stainless steel shafting) to transport stamped steel sheets from a press to a stacking station. To release the parts you don't have to "turn off" the magnets. All you have to do is separate your articles from them.
I did that with an array of pushrods, or fingers, positioned above the sheet flow path. They were linked together so that on signal they all extended downward simultaneously. If there was no release signal, the transported sheet would pass beneath the pushrods unaffected. Each sheet was supported by several magnetic rollers at any given time. The pushrods were arranged to insure separation from all the magnets simultaneously to keep the sheet from tilting. The pushrod array mechanism was actuated by a single cylinder. You could have such an array over each secondary conveyor.