I have a six node cluster: 2 master nodes and 4 client / data nodes.  I 
have two indicies.  One with data and one that is set aside for future 
use.  I'm having trouble with the indicie that is in use.
After making some limits.conf configuraiton changes and restarting the 
impacted nodes, one of my indicies' replica shard will not complete 
initialization.
I wasn't in charge of the node restarts and here is the sequence of events:
Shut down the client and data nodes on each of the four servers.
Start the client and data node on each server.
I don't believe time was allowed to allow the cluster to reallocate or to 
move shards.

limits.conf changes: 
- memlock unlimited
hard nofiles 32000
soft  nofiles  32000

Here's what I have tried thus far:

Drop the replica shard, which brings the cluster status to Green.  
Verify the cluster's status - no replication, no realocating, etc.  
Re-add the replica shard.  

Drop the replica shard and the data nodes that were to carry the replica 
shard.  
Verify the cluster's status.  
Start the data nodes and allow the cluster to reallocate primary shards.  
 - The cluster's status is Green.
Add the replica shard to the indicie.  The replica shard never completes 
initialization, even over a 24 hour period.

I've checked the transaction log files on each node and they are all zero 
legnth files.
The replica shard holding nodes are primary shards for the unused indicie.
These nodes copied it's matching primary node's index Size (as seen in 
paramedic), but now Paramedic shows an index Size of only a few bytes.  The 
index folder on the replica shard servers still has the data.

Unknown to me, my target system was put online and my leadership doesn't 
want to schedule an outage window.  Most my reasearch suggests that I drop 
the impacted indicie and re-initialize.  I can replace the data, but this 
would impact the user interface while the indicie re-ingests the 
documents.  This issue has occured before on my test system and the fix was 
to rebuild the index.  However I never learned why the replica shard had 
the issue in the first place.

My questions are:
- Does the replica shard hosting server's index Size (shown in paramedic) 
indciate a course of action?
- Is it possible to resolve this without dropping the indicie and 
rebuilding?  I'd hate to resort to this each time we attempt ES server 
maintenance or configuration changes.

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