Breaking a pipe while a connected pipe is going to be sending an item to the broken pipe causes a world-breaking bug. Not sure what more help I can offer, but I do have this crash report! Short story long: sent an item from a chest into one of my CrissCross machines, and it was sending them off just fine. But, after one had been sent off (but before arriving to my machine), I broke a pipe in the connection and got this once the item arrived to what used to be the meeting point of the now broken pipe.

Oh, that's silly.