@lovejoy,
You don't say what software it is, but typically this means it will delete the files. With most AV software, the "Vault" or "Quarantine" is like a the Trash/Recycle bin. Instead of things the software finds just being deleted with no way to undo it, they restrict the files so that they can't harm the computer and let you undo the quarantine, attempt to repair the files (sometimes a regular file is infected), or delete them.
So emptying the vault usually means deleting the items the software has quarantined.