Your agent and escrow officer should be working on this matter for you, because it COULD delay closing.
However, I have had many sellers in the same situation, and it's worked out fine. Please have your escrow officer and Realtor talk to your HOA and make sure that the HOA knows that the deficiency or amount owed will be paid off at the close of escrow. That way, the HOA will know that you are working on the issue. The HOA might then be more willing to slow down the process of putting a lien on the home, etc...
Once your escrow officer orders the HOA sales package, your escrow officer should have a demand from the HOA that addresses this matter, the amount owed, etc. You will be able to see what the HOA needs to have done/completed or paid before closing by that document.
If it is something that is bothering you, I encourage you to talk to your Realtor and to your escrow officer and to ask for a copy of the HOA demand as soon as this item is available. Your escrow officer and Realtor should know how to proceed after receiving this document.