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
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?
As we can see, LUCENE-5541 still an open bug, which means the error would still happen even on the latest version of Lucene.
Besides that, have you tried all the information from the KB:
A simple test to check if this is related to any environmental aspect is to set up a test instance and load up the Production XML backup. See if you can reproduce the error.
I hope that this helps. Cheers!
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