Thanks Erick. As I understand now that the entire cluster goes down if any
one shard is down, my first confusion is clarified. 

Following are the other details 

We really need to see details since I'm guessing we're talking
past each other. So:
*1> exactly how are you indexing documents?*
     /using HTTPSolrServer and placing all update request to leader1/shard1.
Enabled autoCommit with 60 seconds and not placing any commit from client
application./
*2> exactly how are you assigning a UUID to a doc?*
     /defined an unique field in schema.xml and it is generated by the
client application, ID format is {mongoDBHostName}-{mongoDBName}-{UUID}. /
*3> do you ever re-index documents? If so, how are you
   assuring that the UUID generated for any re-indexing operations
   are the same ones used the first time? *
/Yes we are re-indexing documents. We are getting the UUID from mongodb and
the ID generated is same while we are doing update as well, using the same
code. /


We are unable to guess the root cause for having duplicate documents in
multiple shards.  Also, it looks reindexing is the only solution for
removing the duplicates.



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