[repacker] fix bug where nodes with incoming virtual links could get orphaned. When attempting to fix overflows nodes that have incoming edges from more than one parent can be duplicated. However, if all of these incoming links are virtual except for one duplicating it will effectively orphan it (one of the copies will be pointed to only by virtual links). Since parent book keeping is expensive we don't want to separately track virtual/real parents so instead just don't duplicate nodes that have at least one incoming virtual link.