For proper index introspection, you can use the lucene tools available from apache. Neo4js lucene indexes are located under [dbdir]/index.
Is the issue just that nodes you expected to be indexed are not showing up? Make sure the batch inserter is properly closed to ensure flushing to disk, and keep an eye out for exceptions.
If problem persists, could you cycle back with the version of neo4j you are using, and perhaps a code sample that demonstrates the issue?
Jake
Sent from my phone, please excuse typos and brievety.
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