Answer:
You basically have two different issues. First, the amount of money due you under the lease is a matter for the bankruptcy court. Second. Their filing document has nothing to do with the lease document. The fact that they made a particular claim to the court on a document is irrelevant as to whether or not they have honored the terms of the lease. No one ever said the law was simple. Many people have been thrown out of leased quarters after declaring bankruptcy for non payment of a lease.
So they owe you money and they want the court to rule that they can continue staying for free. You are wondering if simply because they asked if you have to agree. If they said, "Jump." Would you reply, "How high?" on the way up?
Putting in your claim for money when their assets are sold or whatever the judge decides and letting them stay for free are two separate issues. If there is enough money involved, perhaps you should see a real lawyer.