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Only a guess. Please take a look at vCenter Server Appliance checking for update hangs. Although related to the vCenter Server appliance, you may try to see whether this also works for the Replication Appliance.
I tried that out and had high hopes for it. Unfortunately it still didn't want to work for me, and seeing as how I do not have enough experience with Linux I could not make the offline repository. I ended up un-registering the appliance from vCenter and deploying the updated one.
This was the solution for my problem during virtual appliance upgrade from 5.8.2 to 6.1.
If you have a support request about the issue reported in March, please give me the support request #.