If you relied on instructions that havent been updated yet, then you may end up with an amendment, is it not allowing you to EFile it or is it just a warning diagnostic?

There aren't typically a lot of tax calculations included on an 1120S return.  I don't think there is an enormous amount of risk associated with filing the return.  Grab a pair of scissors and run like the wind and when you are tired of running, hit the send button on the return.