I too have experience the config error thats not a config error in regards to using the persisted queue. I have also witnessed the queue fill up when my three logstash nodes were doing well under the events per second out that my elasticsearch cluster has demonstrated it can do in. When this happened, there was no log output and no data ingestion at all. I had hundreds of queue files and all the logs for elasticsearch and logstash were business as usual. However, all the beats clients reported a connection timeout. I restarted logstash and got the dreaded seq error and went back to the in-memory queue at which everything started flowing again.
I can also replicate the issue very easily by either config testing on the same host as the logstash instance running with persisted queue or by having the auto reload enabled and reloading the pipeline. I wasn't expecting however to have the queue fill up and then generate the error even though I had been purposeful in not reloading the config or running a config test while logstash was up.