One of master pod is not getting restarted

I have deployed ECK 1.3.0 in GCP with 2 master and 3 data-ingest nodes. For backup purpose, referenced secret in secure settings in elasticsearch file and re applied. All the data-ingest and one of master pods are restarted. Only one master pod is not getting restarted. I have to made to restart manually . Could anyone suggest me how to get rid of this problem

The operator does not restart a Pod as long as some conditions are not met. Having the operator logs would help to understand why it was the case in your situation.

Below were the operator pod logs

{"log.level":"info","@timestamp":"2021-02-02T15:22:16.649Z","log.logger":"association.kb-es-association-controller","message":"Ending reconciliation run","service.version":"1.3.0+6db1914b","service.type":"eck","ecs.version":"1.4.0","iteration":1,"namespace":"elk-svc-510","kb_name":"kibana-config","took":0.170393058}
{"log.level":"info","@timestamp":"2021-02-02T15:22:16.821Z","log.logger":"observer","message":"Creating observer for cluster","service.version":"1.3.0+6db1914b","service.type":"eck","ecs.version":"1.4.0","namespace":"elk-svc-510","es_name":"elasticsearch-config"}
{"log.level":"info","@timestamp":"2021-02-02T15:22:25.950Z","log.logger":"generic-reconciler","message":"Updating resource","service.version":"1.3.0+6db1914b","service.type":"eck","ecs.version":"1.4.0","kind":"ConfigMap","namespace":"elk-svc-510","name":"elastic-licensing"}
I0202 15:22:27.000454       1 request.go:621] Throttling request took 1.043926284s, request: GET:https://172.24.0.1:443/apis/pxc.percona.com/v1-6-0?timeout=1m0s
I0202 15:22:37.050354       1 request.go:621] Throttling request took 5.94614821s, request: GET:https://172.24.0.1:443/apis/servicenetworking.cnrm.cloud.google.com/v1beta1?timeout=1m0s
{"log.level":"info","@timestamp":"2021-02-02T15:22:47.029Z","log.logger":"driver","message":"Could not update cluster license","service.version":"1.3.0+6db1914b","service.type":"eck","ecs.version":"1.4.0","err":"while getting current license level 503 Service Unavailable: ","namespace":"elk-svc-510","es_name":"elasticsearch-config"}

The operator logs failed predicates, some logs seem to be missing.

Looks like the cluster was not available, it does prevent the Pods from being restarted. I would have a look at the Elasticsearch cluster logs to understand where this 503 comes from.