In Virginia, if the nolle prosequi before evidence is given in court doesn't bar the commonwealth from refiling those charges (they just have to start over as log as they are still within the statute of limitations).
An amusing piece of appellate law in Virginia. If you are convicted of a misdemeanor in general district court, your first appeal step is a trial de novo. As soon as you file that your original conviction is dismissed. The commonwealth can nolle prosequi the original charges and refile them at this point without triggering the double jeopardy provisions.
All a "direct indictment" means is the commonwealth's attorney is going to file directly with the grand jury rather than allowing the charges to spring from an arrest warrant as the charging document. This is pretty common when refiling after a nolle prosequi or other times when they don't feel they need to take someone into custody first.