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We upgraded all the Hibernate libraries, but nothing seems to make things better.
So what are you using now? latest Hibernate Search 4.2.0.Final, Apache Lucene 3.6.2 and Hibernate ORM 4.1.9.Final ?
I have seen this error before, it is not very common so it's puzzling that you get it regularly. In the cases I've seen it it happens because the node you are restarting happens to initialize the index with bad timing: at the same time a commit is applied on another index.
This should never happen if you use the background copying process with JMS as suggested in the reference documentation; how does your clustering setup look like? which filesystems are being used?