From what you quoted, it sounds as if the schools normally do not accept anything after the first "version" of the form. As such, it would be my guess that they will only put the first form sent in your file. Was the form exactly the same or did you make changes and re-submit? I would think how you handle it now might be different based on the answer to that question.
In the original post, you said it only happened at one school, however the 2nd post suggests it was more than one. I am not sure which is accurate. If it is only one, I would contact that school directly. (BTW this could be done with a letter or email explaining what happened, even if the school doesn't reply, it should be put in your file so anyone looking at you application with a question would see your note). If it is more than one school, I might try and get clarification from the Gateway people because it would be easier for you to solve the problem for all the schools at the source of the problem.
Alternatively, you could simply assume based on the original reply from Gateway that the first version submitted is the form to go with and just proceed from there.
As for starting your applications, all of my child's applications (and our parent portions) were written on the computer first for editing and spelling purposes. Later, the answers were cut and pasted into the applications. I don't know if things have changed in how Gateway works since my child applied but I see no reason why you couldn't start drafting your application answers while you solve this problem.