Hello Shawn, I managed to finally find the issue.
The zoo.cfg in Zookeeper and Solr was different and there was an autopurge option enabled in Zookeeper. After removing the autopurge option and aligning the zoo.cfg in Zookeeper and Solr, the configs and aliases no longer went missing after server restart. Thanks for your help :). A.Guptar -- Sent from: http://lucene.472066.n3.nabble.com/Solr-User-f472068.html