I have to be honest, this is why devices like the ZW, ZW-L, Z4000, and I'm sure other multi-channel single core transformers are much more ideal. By design, the multiple channels are in phase from a single power source.
Edit, in American flyer, ideally use a dual channel transformer like a 30B or some other typical 2 channel transformer.
You don't have the risk of back feeding another transformer that might be unplugged, you don't have to concern phasing multiple transformers, you just have single device that is much safer and easier in this aspect IMO.
Not trying to sell you on a different transformer, I realize you have what you have, but also be aware the situation you appear to be describing has a potentially lethal problem as you have described it.
