Some hard system faults, error during upgrades, migration issues and some other factors may corrupt the index. Most likely end customers would like the production systems to fix index issues in run-time, without delays and restarts. Current versions of JCR supports "Hot Asynchronous Workspace Reindexing" feature. It allows end-user (Service Administrator) to launch the process in background without stopping or blocking whole application by using any JMX-compatible console (see screenshot below, "JConsole in action").

Server can continue working as expected while index is recreated. This depends on the flag "allow queries", passed via JMX interface to reindex operation invocation. If the flag set, then application continues working. But there is one critical limitation the end-users must be aware. Index is frozen while background task is running. It meant that queries are performed on index present on the moment of task startup and data written into repository after startup won't be available through the search until process finished. Data added during re-indexation is also indexed, but will be available only when task is done. Briefly, JCR makes the snapshot of indexes on asynch task startup and uses it for searches. When operation finished, stale indexes replaced by newly created including newly added data. If flag "allow queries" is set to false, then all queries will throw an exception while task is running. Current state can be acquired using the following JMX operation:
getHotReindexingState() - returns information about latest invocation: start time, if in progress or finish time if done.