Rob,
I recommend that you go to the clerk of the court in the county where you had this work done. Ask someone in that office to explain the procedure for filing and perfecting liens.
In general, everyone in Virginia who works and/or supplies material on a property has lien rights. They can pursue their lien rights if they don't get paid in full.They have these lien rights even before an invoice is presented to you or the owner of the property.
The lien will be placed against the property, not against you personally. And I am assuming that this was a job you had done for your customer? If so, then the issue ultimately will be theirs to deal with because their property will be the object of the lien.
I recommend getting out ahead of this. Communicate in writing to this subcontractor and keep your customer informed. Again, ultimately it will be their problem to deal with because it is their property at stake.
In the meantime, check with DPOR to make sure these guys have a valid contractor's license, check with the county where the job was performed to ensure they have the required local business license, and check with the Clerk's office of the State Corporation Commission to see how the business is registered and who is listed as the responsible party.
Did you get certificates of insurance, for both business liability and workman's comp? If not, I would get them now as part of this process of making the final payment because once this is settled and the final payment has been made you will have a hard time getting this information from them.
Good luck. It's a real joy being a GC, eh?