Someone will have to pay the HOA something in order to provide the new buyer with clear title and to get the deal closed.
In a short sale, making sure that clear title is provided, is the responsibility of you and your Realtor.
If you cannot pay the back due dues yourself, you have some options for help.The first place to go looking for help is the lender/servicer that owns your first loan. They almost always pay the HOA some, if not all (depending on what you owe,) of the past due fees.
If the amount your lender/servicer is willing to pay is not enough to get the HOA to settle and release their lien, then you and your Realtor need to get creative.
You can ask the buyer to help out. Sometimes buyers are willing to pay the back dues or, at least, pay enough to get the HOA to release the lien.
Any way you look at it, HOAs generally don't just go away. They will want something from someone. Find out what it will take to get them to settle and release their lien, then work with your Realtor, lender/servicer, the buyer's agent, and the buyer, to make it happen.
There are two important issues:
It is in your best interest to get them to settle. If all they are willing to do is release the lien, then they maybe leaving the option of pursuing you for the remainder owed, open. If they settle, you will not be pursued for the remainder.
If the lender/servicer is not able to pay everything the HOA wants, they must agree to whatever terms you and your Realtor have worked out to get the HOA to settle. In example, if the buyer is going to help, the first must say it is ok for them to do so.