I know this is an old post, but I had to submit a reply based off something I found to be my issue with this particular subject. I recently modified the search peers via the deployer for my SHC and later come to realize the search peer configuration didn't take on all the members of the SHC. I'm currently running three members and each of them had a different list of search peers, but a combination of what the actual list of search peers were. I just had to do a rolling restart on the SHC and everything went back to normal and search peer distribution was corrected. I'm not sure if it was an issue with the deployer not restarting Splunk on all the members or what, but that resolved my issue. You can look at the DMC view Search > Search Head Clustering > Search Head Clustering: Status and Configuration to verify.
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