I answer to myself.

Before to do the setXXX(), I must delete the previous object.

Like this : 

POJOUser user = pm.getObjectById(POJOUser.class, username);
pm.deletePersistent(user.getLastLocation());
user.setLastLocation(new POJOLocation(newLocation));

And now, it works. Moreover, old references are deleted of the store.

I hope this tips will help someone.

Yoann

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