In two recent short sales with Bank of America, extra payment was required from the buyer so the bank would "grant deficiency waiver." The amount, $92,000 will not appear anywhere as the acquisition cost of the house.
There is way too much we do not know about your specific situation to provide precise responses. Your real estate professional will be able to guide you through this process.
Best of success in acquiring your new home,
ReMax Realtec Group
Palm Harbor, FL
727. 420. 4041
If it's a bank owned or regular sale your contract will control your costs and you should be able to enforce the terms of your contract pretty easily.
If it's a Short Sale, it's not unusual to have extraordinary costs or you may not be able to close. Even if your Short Sale contract says the condo/HOA fees to bring it current will be paid by the Seller, some lenders will not allow more than one years back due and also limit the HOA/Condo attorney fees, too. Most Short Seller will simply sell to another buyer if you're not able to pay the extraordinary fees required.
All the best,