Elasticsearch version (bin/elasticsearch --version):
5.6.5 (5.6.4 works fine, so maybe related to #27534 and #27516 and #20498 )

Plugins installed: []

JVM version (java -version):
java version "1.8.0_121"
Java(TM) SE Runtime Environment (build 1.8.0_121-b13)
Java HotSpot(TM) 64-Bit Server VM (build 25.121-b13, mixed mode)

OS version (uname -a if on a Unix-like system):
Mac and Ubuntu

Description of the problem including expected versus actual behavior:
"java.lang.AssertionError: map must be empty" when it not must be thrown

Steps to reproduce:

• Make sure assertions are enabled (export ES_JAVA_OPTS=-ea)
• Delete a non existent document in an non existent index (curl -Ss -XDELETE "http://localhost:9200/x/y/1")
• Make a synced flush (curl -Ss -XPOST "http://localhost:9200/_flush/synced")

Provide logs (if relevant):

[2017-12-17T15:24:39,706][ERROR][o.e.b.ElasticsearchUncaughtExceptionHandler] [] fatal error in thread [elasticsearch[Cj7lPWN][flush][T#3]], exiting
java.lang.AssertionError: map must be empty
	at org.elasticsearch.index.engine.LiveVersionMap.adjustMapSizeUnderLock(LiveVersionMap.java:43) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.index.engine.InternalEngine.syncFlush(InternalEngine.java:997) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.index.shard.IndexShard.syncFlush(IndexShard.java:757) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.indices.flush.SyncedFlushService.performSyncedFlush(SyncedFlushService.java:423) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.indices.flush.SyncedFlushService.access$1100(SyncedFlushService.java:70) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.indices.flush.SyncedFlushService$SyncedFlushTransportHandler.messageReceived(SyncedFlushService.java:704) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.indices.flush.SyncedFlushService$SyncedFlushTransportHandler.messageReceived(SyncedFlushService.java:700) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.transport.TransportRequestHandler.messageReceived(TransportRequestHandler.java:33) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.transport.RequestHandlerRegistry.processMessageReceived(RequestHandlerRegistry.java:69) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.transport.TransportService$7.doRun(TransportService.java:654) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.common.util.concurrent.ThreadContext$ContextPreservingAbstractRunnable.doRun(ThreadContext.java:638) ~[elasticsearch-5.6.5.jar:5.6.5]
	at org.elasticsearch.common.util.concurrent.AbstractRunnable.run(AbstractRunnable.java:37) ~[elasticsearch-5.6.5.jar:5.6.5]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[?:1.8.0_121]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[?:1.8.0_121]
	at java.lang.Thread.run(Thread.java:745) [?:1.8.0_121]