Index rows in the database are not being deleted when the deleted_ flag is set to 1. The reason appears to be that the code in JdbcDirectory.deleteMarkDeleted() runs successully, but the transaction is immediately rolled back because autoCommit is set to false (the default).
I am using MySQL 5.0.24a and MySQL Connector/J 3.1.13.
Fixed for version 1.2 M, and created a new patch version 1.1.1