I encountered the same problem last week.
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My case was (on hbase 0.94.9) that a zoo.cfg was put under ./hbase/conf.
I was thinking about to open a jira for the sanity check (exactly the same idea), and glad to find this jira before opening a dup.
Just curious that why this jira hasn't been pushed into trunk and 0.94 yet since no strong objection in the comments. Well, understand that this is a rare case, but a couple line of code can save someone(like me) several hours of debugging, which sounds a good idea.
The jira is still unassigned. I can do some testing and upload an up-to-date patch (both trunk and 0.94) if everyone is busy.
P.S. per the comments about checking 'addPeer'. I tried it(add_peer with zookeeper info of the master cluster), which won't cause the UUID case in replicateSource. So far, the only case I am aware of is the one reported with incorrect zoo.cfg