Resolution:
The following is a workaround to export the repository instance in chunks. When importing the individual chunks, a specific sequence has to be followed to restore the instance to its original content.  Doing it in chunks will shorten the export/import time.

1. Export each branch of the repository independently of each other, allowing for a clean export. This can be done by adding the -nochase flag, and modifying the export parameters you pass to the repositoryexport script to include the branch you are interested in.  For example:

repositoryexport -nochase -url tibcr://BCTM-DEV:service=7514
c:\temp\BCTM-DEV-public.exp /tibco/public

repositoryexport -nochase -url tibcr://BCTM-DEV:service=7514
c:\temp\BCTM-DEV-private.exp /tibco/private

This generates two separate export files for each branch of the BCTM-DEV repository, and stores them in the C:\temp directory (this can be changed as needed).

2. Re-importing the files can be done using the following commands:

repositoryimport -overwrite -url tibcr://BCTM-DEV-DB:service=7514
c:\temp\BCTM-DEV-public.exp

repositoryimport -overwrite -url tibcr://BCTM-DEV-DB:service=7514
c:\temp\BCTM-DEV-private.exp

If you don't import the files in the proper order, you may get some errors when you import the first file.  This is because the private branch is trying to reference public branches that are not yet created.  

Another caution: if you have Parent-child references in ADB agents, or custom schemas created for MB, re-import the public class for a second time after completing the above process.  This will ensure that all relative links are correctly written to the new repository instance.

Note in Administrator 5.0, we have eliminated the slow export problem by splitting the RV messages sending node information from server to client into chunks.  It is possible to generate a 50 MB export file in 30 seconds.