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The message is an indication that locks aren't being properly cleaned up/released from the system area. More precisely, the locks appear as missing from the repository - i.e. they have been deleted - but the parent which owns them still has references to them. This should not affect the repository behavior, but it could be the indication of a bug.
Since you're using an older version of ModeShape, it's hard to tell what the problem is. Ideally, if you can move to the latest ModeShape (4.2) and replicate this behavior, opening an issue would help us track down the problem. It may also happen that this issue has been fixed in ModeShape 4, since we've corrected several lock-related issues([MODE-2190] Lock Garage Collection can cause NPE as locks are removed by sessions - JBoss Issue Tracker, [MODE-2342] Remove lock tokens from sessions upon logout(). - JBoss Issue Tracker, [MODE-2370] Session scoped locks broken in 3.8.x with JTA - JBoss Issue Tracker etc)
In the meantime I've opened https://issues.jboss.org/browse/MODE-2450 and we'll actually cleanup those phantom locks starting with ModeShape 4.3