I flushed entitymanager twice (using autoflush) in one transaction.
First flush ended in ModWorkUnit with 3 modified attribute flags set to true
Second flush ended in ModWorkUnit wih 1 modified attribute flag set to true.

Merge of these two ModWorkUnits ended in ModWorkUnit with corrent entity, but only with 1 modified attribute flag set to true.

I suppose this is because this method:

public AuditWorkUnit merge(ModWorkUnit second) { return second; }

I thing mod flags should be set again by comparing second ModWorkUnit with state of entity before first ModWorkUnit.