Fix Inconsistencies in the repository when SegmentNotFound Issue is reported in AEM 6.x

Download a version of oak-run that matches your oak core version from https://mvnrepository.com/artifact/org.apache.jackrabbit/oak-run

To revert a corrupt segment store to its latest good state change into CQ's working directory (the one containing the crx-quickstartfolder) and backup all files in ./crx-quickstart/repository/segmentstore/.

Run the consistency check,
java -Xmx6000m -jar oak-run-*.jar check --bin=-1 /path/to/crx-quickstart/repository/segmentstore

This searches backwards through the revisions until it finds a consistent one:
Look for message like below:
[main] INFO o.a.j.o.p.s.f.t.ConsistencyChecker - Found latest good revision afdb922d-ba53-4a1b-aa1b-1cb044b535cf:234880

Revert the repository to this revision by editing ./crx-quickstart/repository/segmentstore/journal.log and deleting all lines after the line containing the latest good revision.

Remove all ./crx-quickstart/repository/segmentstore/*.bak files.

Run checkpoint clean-up to remove orphaned checkpoints:

java -Xmx6000m -jar oak-run-*.jar checkpoints /path/to/crx-quickstart/repository/segmentstore rm-unreferenced

Finally compact the repository:

java -Xmx6000m -jar oak-run-*.jar compact /path/to/crx-quickstart/repository/segmentstore/