Don’t modify anything within the data directory or run processes that might interfere with its contents. If something other than Elasticsearch modifies the contents of the data directory, then Elasticsearch may fail, reporting corruption or other data inconsistencies, or may appear to work correctly having silently lost some of your data. Don’t attempt to take filesystem backups of the data directory; there is no supported way to restore such a backup. Instead, use Snapshot and restore to take backups safely. Don’t run virus scanners on the data directory. A virus scanner can prevent Elasticsearch from working correctly and may modify the contents of the data directory. The data directory contains no executables so a virus scan will only find false positives.
Yes, modifying the contents of the data directory (e.g. by removing a file) is very harmful to Elasticsearch.
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