Fix bug affecting SubProcesses

Fix a bug affecting SubProcesses. It affects
them when input files are being merged and
the input files have differing BranchIDLists
and the SubProcess produces something.
An attempt to use a Ref or Ptr in the SubProcess
or any subsequent job using its output can result
in a failed assert which aborts the job. The
BranchListIndexes which are used to reference
Ref's become corrupt.