Why not just re-index while the instance is up?
1) Go to /system/console/status-oak-index-stats and make note of the indexes that are corrupted and while indexing lanes are corrupted.
2) Go to /system/console/slinglog and define an INFO level logger for org.apache.jackrabbit.oak.plugins.index.IndexUpdate and have it write to its own file
3) Go to the JMX console /system/console/jmx
4) Find the CheckpointManager mbean
5) Invoke the listCheckpoints() method -- it will print a table of checkpoints and their id numbers -- there will be at-least 2 rows, there could be more.
6) Make note of the checkpoint Id numbers for the lanes that are corrupted -- put these id's in a text file
7) invoke the releaseCheckpoint(java.lang.String p1) method -- passing in a single id from your text file at a time.
8 ) Go to /crx/de -- /oak:index/<whatever the corrupted index is>
9) Change the boolean 'reindex' property to true.
10) Save and repeat 8-9 for all indexes listed in step 1
11) tail the log from step 2
Good luck