We found this issue when running large scale ingestion tests for
HBASE-5754. The problem is that the .META. table updates are not atomic while splitting a region. In SplitTransaction, there is a time lap between the marking the parent offline, and adding of daughters to the META table. This can result in clients using MetaScanner, of HTable.getStartEndKeys (used by the TableInputFormat) missing regions which are made just offline, but the daughters are not added yet.
This is also related to