I turned on full debugging and set <property name="hibernate.jdbc.batch_size">0</property>  
Now a huge output comes and I tried to cut out the relevant pieces:
at beginning:
Code:
     [java] 65634 [main] DEBUG org.hibernate.engine.PersistenceContext  - initializing non-lazy collections
     [java] 65634 [main] DEBUG example.hibernateutils.HibernateUtilImport  - Opening new Session for this thread.
     [java] 65634 [main] DEBUG org.hibernate.impl.SessionImpl  - opened session at timestamp: 4558690471817216
     [java] 65634 [main] DEBUG example.hibernateutils.HibernateUtilImport  - Starting new database transaction in this thread.
     [java] 65634 [main] DEBUG org.hibernate.transaction.JDBCTransaction  - begin
     [java] 65635 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - opening JDBC connection
     [java] 65635 [main] DEBUG org.hibernate.connection.DriverManagerConnectionProvider  - total checked-out connections: 0
     [java] 65635 [main] DEBUG org.hibernate.connection.DriverManagerConnectionProvider  - using pooled JDBC connection, pool size: 0
     [java] 65635 [main] DEBUG org.hibernate.transaction.JDBCTransaction  - current autocommit status: false
     [java] 65635 [main] DEBUG org.hibernate.engine.Cascades  - id unsaved-value strategy NULL
     [java] 65635 [main] DEBUG org.hibernate.event.def.AbstractSaveEventListener  - detached instance of: example.Prim
     [java] 65635 [main] DEBUG org.hibernate.event.def.DefaultSaveOrUpdateEventListener  - updating detached instance
     [java] 65635 [main] DEBUG org.hibernate.event.def.DefaultSaveOrUpdateEventListener  - updating [example.Prim#1aA1]
     [java] 65635 [main] DEBUG org.hibernate.event.def.ReattachVisitor  - collection dereferenced while transient [example.Prim.HasPrim#1aA1]
     Code:
     [java] 76247 [main] DEBUG org.hibernate.event.def.DefaultSaveOrUpdateEventListener  - updating [example.Prim#32bD7]
     [java] 76247 [main] DEBUG example.hibernateutils.HibernateUtilImport  - Committing database transaction of this thread.
     [java] 76247 [main] DEBUG org.hibernate.transaction.JDBCTransaction  - commit
     [java] 76247 [main] DEBUG org.hibernate.impl.SessionImpl  - automatically flushing session
     [java] 76247 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - flushing session
     [java] 76247 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - processing flush-time cascades
     [java] 76280 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - dirty checking collections
     [java] 76280 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - Flushing entities and processing referenced collections
     [java] 76288 [main] DEBUG org.hibernate.event.def.DefaultFlushEntityEventListener  - Updating entity: [example.Prim#1aA1]
     [java] 76288 [main] DEBUG org.hibernate.event.def.DefaultFlushEntityEventListener  - Updating entity: [example.Prim#1aA10]
     [java] 76288 [main] DEBUG org.hibernate.event.def.DefaultFlushEntityEventListener  - Updating entity: [example.Prim#1aA11]
     [java] 76288 [main] DEBUG org.hibernate.event.def.DefaultFlushEntityEventListener  - Updating entity: [example.Prim#1aA12]
     [java] 78260 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - Processing unreferenced collections
     [java] 78260 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - Scheduling collection removes/(re)creates/updates
     [java] 78260 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - Flushed: 0 insertions, 6231 updates, 0 deletions to 6231 objects
     [java] 78260 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - Flushed: 0 (re)creations, 0 updates, 6231 removals to 0 collections
       [java] 78261 [main] DEBUG org.hibernate.pretty.Printer  - example.Prim{name=null, id=10aE12, content=52.0, HasPrim=null, seq=xxxxx, temp=64.6}
     [java] 78261 [main] DEBUG org.hibernate.pretty.Printer  - example.Prim{name=null, id=3aH6, content=58.3, HasPrim=null, seq=xxxxx, temp=66.1}
           at the end:
Code:
     
     [java] 78266 [main] DEBUG org.hibernate.pretty.Printer  - more......
     [java] 78266 [main] DEBUG org.hibernate.event.def.AbstractFlushingEventListener  - executing flush
     [java] 78278 [main] DEBUG org.hibernate.persister.entity.BasicEntityPersister  - Updating entity: [example.Prim#1aA1]
     [java] 78278 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - about to open PreparedStatement (open PreparedStatements: 0, globally: 0)
     [java] 78278 [main] DEBUG org.hibernate.SQL  - update primer set name=?, seq=?, temp=?, content=? where id=?
     [java] Hibernate: update primer set name=?, seq=?, temp=?, content=? where id=?
     [java] 78278 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - preparing statement
     [java] 78278 [main] DEBUG org.hibernate.persister.entity.BasicEntityPersister  - Dehydrating entity: [example.Prim#1aA1]
     [java] 78279 [main] DEBUG org.hibernate.type.StringType  - binding null to parameter: 1
     [java] 78279 [main] DEBUG org.hibernate.type.StringType  - binding 'xxxx' to parameter: 2
     [java] 78279 [main] DEBUG org.hibernate.type.FloatType  - binding '61.3' to parameter: 3
     [java] 78279 [main] DEBUG org.hibernate.type.FloatType  - binding '44.0' to parameter: 4
     [java] 78279 [main] DEBUG org.hibernate.type.StringType  - binding '1aA1' to parameter: 5
     [java] 78310 [main] ERROR org.hibernate.event.def.AbstractFlushingEventListener  - Could not synchronize database state with session
     [java] org.hibernate.HibernateException: Unexpected row count: 0 expected: 1
     [java]     at org.hibernate.jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:32)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.update(BasicEntityPersister.java:1995)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.updateOrInsert(BasicEntityPersister.java:1923)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.update(BasicEntityPersister.java:2163)
     [java]     at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:75)
     [java]     at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:239)
     [java]     at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:223)
     [java]     at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:137)
     [java]     at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:274)
     [java]     at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
     [java]     at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:675)
     [java]     at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:293)
     [java]     at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:86)
     [java]     at example.hibernateutils.HibernateUtilImport.commitTransaction(HibernateUtilImport.java:187)
     [java]     at example.dao.GenericServiceDAOImport.commit(GenericServiceDAOImport.java:46)
     [java]     at example.transformer.CloneTransformer.makePrimer(CloneTransformer.java:161)
     [java]     at example.Loader.<init>(Loader.java:29)
     [java]     at example.Main.main(Main.java:9)
     [java] 78330 [main] DEBUG example.hibernateutils.HibernateUtilImport  - Tyring to rollback database transaction of this thread.
     [java] 78330 [main] DEBUG org.hibernate.transaction.JDBCTransaction  - rollback
     [java] 78330 [main] DEBUG org.hibernate.jdbc.JDBCContext  - before transaction completion
     [java] 78330 [main] DEBUG org.hibernate.impl.SessionImpl  - before transaction completion
     [java] 78338 [main] DEBUG org.hibernate.transaction.JDBCTransaction  - rolled back JDBC Connection
     [java] 78339 [main] DEBUG org.hibernate.jdbc.JDBCContext  - after transaction completion
     [java] 78339 [main] DEBUG org.hibernate.impl.SessionImpl  - after transaction completion
     [java] 78350 [main] DEBUG example.hibernateutils.HibernateUtilImport  - Closing Session of this thread.
     [java] 78350 [main] DEBUG org.hibernate.impl.SessionImpl  - closing session
     [java] 78350 [main] DEBUG org.hibernate.jdbc.AbstractBatcher  - closing JDBC connection (open PreparedStatements: 1, globally: 1) (open ResultSets: 0, globally: 0)
     [java] 78350 [main] DEBUG org.hibernate.connection.DriverManagerConnectionProvider  - returning connection to pool, pool size: 1
     [java] 78350 [main] DEBUG org.hibernate.jdbc.JDBCContext  - after transaction completion
     [java] 78350 [main] DEBUG org.hibernate.impl.SessionImpl  - after transaction completion
     [java] org.hibernate.HibernateException: Unexpected row count: 0 expected: 1
     [java]     at org.hibernate.jdbc.NonBatchingBatcher.addToBatch(NonBatchingBatcher.java:32)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.update(BasicEntityPersister.java:1995)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.updateOrInsert(BasicEntityPersister.java:1923)
     [java]     at org.hibernate.persister.entity.BasicEntityPersister.update(BasicEntityPersister.java:2163)
     [java]     at org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:75)
     [java]     at org.hibernate.engine.ActionQueue.execute(ActionQueue.java:239)
     [java]     at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:223)
     [java]     at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:137)
     [java]     at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:274)
     [java]     at org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:27)
     [java]     at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:675)
     [java]     at org.hibernate.impl.SessionImpl.managedFlush(SessionImpl.java:293)
     [java]     at org.hibernate.transaction.JDBCTransaction.commit(JDBCTransaction.java:86)
     [java]     at example.hibernateutils.HibernateUtilImport.commitTransaction(HibernateUtilImport.java:187)
     [java]     at example.dao.GenericServiceDAOImport.commit(GenericServiceDAOImport.java:46)
     [java]     at example.transformer.CloneTransformer.makePrimer(CloneTransformer.java:161)
     [java]     at example.Loader.<init>(Loader.java:29)
     [java]     at example.Main.main(Main.java:9)
     [java] Exception in thread "main" example.exceptions.InfrastructureException
     [java]     at example.hibernateutils.HibernateUtilImport.commitTransaction(HibernateUtilImport.java:192)
     [java]     at example.dao.GenericServiceDAOImport.commit(GenericServiceDAOImport.java:46)
     [java]     at example.transformer.CloneTransformer.makePrimer(CloneTransformer.java:161)
     [java]     at example.Loader.<init>(Loader.java:29)
     [java]     at example.Main.main(Main.java:9)