Filebeat stops harvesting logs

1. Filebeat harvested logs correctly
2. Restarted logstash
3. New logs appear in Kibana
4. After some time, logs are not being harvested from a docker container, although new log entries are written to file

Note that logstash correctly receives logs from other containers harvested by filebeat.
Filebeat harvester didn't recover even after a few hours.

Filebeat configuration:
```
output.logstash:
hosts: ["logstash:5044"]
setup.kibana.host: http://kibana:5601
filebeat.autodiscover:
providers:
- type: docker
hints.enabled: true
```

Docker compose service:
```
web:
image: app:latest
expose:
- 80
labels:
co.elastic.logs/multiline.pattern: '^[[:space:]]+(at|\\.{3})\\b|^Caused by:'
co.elastic.logs/multiline.negate: false
co.elastic.logs/multiline.match: after
app: web
environment:
ELASTIC_APM_SERVER_URLS: http://apm:8200
```

My docker container that is not being harvested has id: **3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c**

This container was also restarted at **2019-09-11 15:19:03,983**.
Last log entry correctly processed has timestamp **2019-09-11 15:19:37,235**.
Next log entry with timestamp **2019-09-11 15:20:15,276** and next ones are missing.

Filebeat relevant log:
```
2019-09-11T15:19:57.988Z INFO [monitoring] log/log.go:145 Non-zero metrics in the last 30s {"monitoring": {"metrics": {"beat":{"cpu":{"system":{"ticks":28150,"time":{"ms":120}},"total":{"ticks":54510,"time":{"ms":150},"value":54510},"user":{"ticks":26360,"time":{"ms":30}}},"handles":{"limit":{"hard":1048576,"soft":1048576},"open":13},"info":{"ephemeral_id":"17c964bc-009e-4840-89b6-4b9c511cdf14","uptime":{"ms":15900511}},"memstats":{"gc_next":8939216,"memory_alloc":4663776,"memory_total":6966547888},"runtime":{"goroutines":93}},"filebeat":{"events":{"active":-2,"added":114,"done":116},"harvester":{"open_files":5,"running":5}},"libbeat":{"config":{"module":{"running":0}},"output":{"events":{"acked":116,"batches":13,"total":116},"read":{"bytes":78},"write":{"bytes":31559}},"pipeline":{"clients":8,"events":{"active":0,"published":114,"total":114},"queue":{"acked":116}}},"registrar":{"states":{"current":10,"update":116},"writes":{"success":13,"total":13}},"system":{"load":{"1":1.19,"15":0.58,"5":0.86,"norm":{"1":0.2975,"15":0.145,"5":0.215}}}}}}
2019-09-11T15:20:04.554Z INFO input/input.go:149 input ticker stopped
2019-09-11T15:20:04.554Z INFO input/input.go:167 Stopping Input: 9894227653855818847
2019-09-11T15:20:04.554Z INFO log/harvester.go:274 Reader was closed: /var/lib/docker/containers/3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c/3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c-json.log. Closing.
2019-09-11T15:20:27.995Z INFO [monitoring] log/log.go:145 Non-zero metrics in the last 30s {"monitoring": {"metrics": {"beat":{"cpu":{"system":{"ticks":28160,"time":{"ms":10}},"total":{"ticks":54610,"time":{"ms":100},"value":54610},"user":{"ticks":26450,"time":{"ms":90}}},"handles":{"limit":{"hard":1048576,"soft":1048576},"open":12},"info":{"ephemeral_id":"17c964bc-009e-4840-89b6-4b9c511cdf14","uptime":{"ms":15930517}},"memstats":{"gc_next":5878912,"memory_alloc":7557664,"memory_total":6986384152,"rss":-2998272},"runtime":{"goroutines":82}},"filebeat":{"events":{"added":31,"done":31},"harvester":{"closed":1,"open_files":4,"running":4}},"libbeat":{"config":{"module":{"running":0}},"output":{"events":{"acked":30,"batches":12,"total":30},"read":{"bytes":72},"write":{"bytes":17806}},"pipeline":{"clients":7,"events":{"active":0,"filtered":1,"published":30,"total":31},"queue":{"acked":30}}},"registrar":{"states":{"current":10,"update":31},"writes":{"success":13,"total":13}},"system":{"load":{"1":1.24,"15":0.6,"5":0.89,"norm":{"1":0.31,"15":0.15,"5":0.2225}}}}}}
```

Logstash restarted timeline log:
```
[2019-09-11T15:16:36,298][INFO ][logstash.runner ] Starting Logstash {"logstash.version"=>"7.3.0"}
..................
[2019-09-11T15:16:45,397][INFO ][logstash.agent ] Successfully started Logstash API endpoint {:port=>9600}
```

Filebeat repository entry:
```
{
"source": "/var/lib/docker/containers/3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c/3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c-json.log",
"offset": 794342,
"timestamp": "2019-09-11T15:20:04.5542604Z",
"ttl": -1,
"type": "container",
"meta": null,
"FileStateOS": {
"inode": 802588,
"device": 2049
}
}
```

Log file stats:
```
sh-4.2# stat 3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c-json.log
File: '3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c-json.log'
Size: 911932 Blocks: 1784 IO Block: 4096 regular file
Device: 801h/2049d Inode: 802588 Links: 1
Access: (0640/-rw-r-----) Uid: ( 0/ root) Gid: ( 0/ root)
Access: 2019-09-11 17:39:48.711393000 +0000
Modify: 2019-09-11 17:19:37.112086700 +0000
Change: 2019-09-11 17:19:37.112086700 +0000
Birth: -
```

Hope I provided enough details to investigate this problem.

----------------------
Elastic stack 7.3.0

Start by reproducing the failure with the Filebeat 7.3.0 Docker autodiscover configuration and inspect the harvester log, registry entry, and container log path for container 3252b7646a23293b6728941769f0412e2bd4b74b801ee09ab747c7cdfa74550c. The report names no source file or test; done means identifying why harvesting stops after the container restart and verifying recovery for subsequent log entries.

Written by the indexing model from the issue text.