user_prefs should not be deployed via deployer remove shcluster/apps/user-prefs, deploy to peers, return to each peer and reinstall the rpm/tar to restore the missing files
A few other things to check
1. review all contents of shcluster/apps ensure install_source_checksum is not present in default|local/apps.conf for any deployed apps if you have to clean up deploy to the cluster after cleanup actions.
2. Make sure the SHC members are not the client of a deployment server, if they are (deploymentclient.conf) remove this file and run a rolling restart. find and remove the deployment client artifacts left in opt/splunk/var
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