This is a post for myself, how to fix this problem. It happens to my Alfresco instance when after power failure some file indexes get borked.

So the error:

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Caused by: java.lang.RuntimeException: Error during run with lock.

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Caused by: java.io.IOException: read past EOF

What happened there was the lucene indexes are messed up. Something dirty, when the power got cut, happened to some of the files. What the solution is:

Rebuild the index.

As simple as that.