Problem with ELK Cluster, Unassigned Shards

Hi, I need help with an ELK cluster. I'm new at this.
I have a cluster formed by 3 Logstash nodes, 3 Elasticsearch nodes and 1 Kibana node.
A week ago the Elasticsearch nodes had no space and didn't let you authenticate in Kibana. Some indexes have been deleted manually in one of the Elasticsearch nodes, I think this action damaged the synchronization between the 3 nodes.
Right now Kibana shows shards errors (unassigned primary and replica) and Logstash can't send logs for shards errors either.
How can I repair the shards and recover the synchronization.
Thanks in advance.

Manually deleting indices from disk on Elasticsearch nodes is NOT supported and can cause all sorts of problems. Which version of Elasticsearch are you using? How many indices and shards do you have in the cluster?

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