If there is something in writing between the owners that indicates the trade was to be effective after week 2, I think you have no choice but to reverse the trade now and reprocess it after week 2.
Even if it wasn't in writing, if Owner B knows that was part of the deal and just wants to pretend it wasn't, he is a bum.
This type of trading should not be allowed, unless you have a complex website running your league that can handle it. It is too much for you, and everyone else, to keep up with. And, it will just lead to problems. If you want to trade, do it now. Otherwise, wait until next week to agree to the deal.