db4o Defragment deletes all objects in the database

I am using db4o 8.0. The db4odatabase file size is 21MB. The database has following Objects in it.

User : There is 1 user in db.
PostedMessage : There are 10000 postedMessages in db.

I delete all 10000 PostedMessages. Then I try to defragment the db4o database. Following code is used for Defragmentation.

private void processDefrag() {
    try {
        String dbpath = "D:\\db4oDatabase";

        IdMapping mapping = new InMemoryIdMapping();
        //new DatabaseIdMapping(dbpath); //use this if heap overflows

        DefragmentConfig config = new DefragmentConfig(dbpath, dbpath+".bak", mapping);
        config.storedClassFilter(new AvailableClassFilter());
        config.forceBackupDelete(false);
        config.objectCommitFrequency(1000);
        Defragment.defrag(config);
        System.out.println("Defrag completed");

    } catch (IOException ex) {
        ex.printStackTrace();
    }
}

My expectation is that the db4oDatabase file size will go back to 21 Kb. And the db4oDatabase will still contain the 1 User object in it. However, after running the above code, the db4odatabase becomes completely empty. Why is it happening like that?

How can I avoid losing the other objects which were not deleted (in this case the 1 User object)? What is the right way of doing defragmentation on db4o database?

If it's not accepting the class because it can't find it, you might try writing a StoredClassFilter of your own that just accepts all StoredClass objects.

public class AcceptAllClassFilter implements StoredClassFilter {

    @Override
    public boolean accept(StoredClass storedClass) {
        return true;
    }
}

Then:

config.storedClassFilter(new AcceptAllClassFilter());

This will work unless the defrag process just deletes everything without a StoredClass automatically. If this is the case, we may need to figure out why the User class doesn't have a corresponding StoredClass instance for the container.