Typically, in a short sale situation, the Seller can not afford to pay HOA fees that are in arrears. When your offer was submitted with the HUD to the lender, hopefully a good estimate of the arrears were included on the HUD to be paid by the lender. To get an exact estimate, the Seller would have to order an estoppel. The estoppel costs money, so an estimate is sometimes used in the beginning of the process.
Usually, the Bank will determine if they are willing to pay the entire amount owed to the HOA or a portion of the amount. Whomever is negotiating the Sellers short sale will find out if the HOA is willing to accept the Lender's offer of payment. If the HOA refuses the Lender's offer, then it may be up to the Buyer to pay the difference (usually by a raise in the purchase price) Properties that are subject to HOA fees add another important element in a short sale negotiation.
Good Luck with your purchase!