We've experienced this error about a 1/2 dozen times over the past 2 or 3 months. A quick search lands us on https://confluence.atlassian.com/jirakb/jira-throws-no-sub-file-with-id-found-when-indexing-755336650.html which points to a lucene bug https://issues.apache.org/jira/browse/LUCENE-5541 that says the problem is lessened in 4.x versions of JIRA.
This confluence article was written in 2015 if the logs in the article are to be believed. Why has lucene not been updated to 4.x in JIRA in the past two years? Our web-inf dir shows version 3.3.0
jira-lucene-dmz-7.3.3.jar
lucene-analyzers-3.3.0.jar
lucene-core-3.3.0-atlassian-1.jar
lucene-extras-3.3.0-atlassian-3.jar
Has anyone else experienced recurring issues with the Lucene index like this? If so how did you fix it? How can we get Atlassian to upgrade the Lucene version to a version that is less prone towards this error?