During region close compacted files which have not yet been archived by the discharger are archived as part of the region closing process. It is important that these files are wholly archived to insure data consistency. ie a storefile containing delete tombstones can be archived while older storefiles containing cells that were supposed to be deleted are left unarchived thereby undeleting those cells.
On region close a compacted storefile is skipped from archiving if it has read references (ie open scanners). This behavior is correct for when the discharger chore runs but on region close consistency is of course more important so we should add a special case to ignore any references on the storefile and go ahead and archive it.
Attached patch contains a unit test that reproduces the problem and the proposed fix.