Wise logic on your part. See a business and real estate lawyer to make sure you do this right. I am not a business lawyer and when I had a similar issue I hired someone to draft all the documents. It just makes sense.
I am not sure I understand your question, but the reality is that no matter what any of us say, it will eventually be up to a judge or jury to decide who pays unless you can resolve it. So you will need to contact local counsel and lay out all the facts in front of them and follow their advice.
Just guessing but if this agreement supersedes all others, there are likely to be some other changes. Otherwise there would be no need for it. Understand your original contract is binding unless you sign this one. You should discuss all of this with the attorney. It might also be worth your money to have a contracts lawyer review and explain the entire contract before you decide whether to sign it.