Good start, you already know which index health value is in RED, which means that index is missing one or more primary shard, please identify them using this great blog post of elastic and see if some of your nodes in cluster is disconnected, holding the primary shards of RED index?
If you can't get back the nodes, holding the primary shards of the index, then as mentioned in the same blog, you have to loose the data and create empty primary shards using reroute API.
In the odd event that all nodes holding copies of this particular shard are all permanently dead, the only recourse is to use the reroute commands to allocate an empty/stale primary shard and accept the fact that data has been lost.
