Thanks Antonius and Gunter.
Gunter, I closed all windows and cleared the memory before taking the backup. If you put all your new models "In session" and open the assembly, everything works fine. The problem is I will be handling big assemblies and can't open and keep all new models in session since i do not know which sublevel parts ae coming inside.
I made a test with ProE and Creo creating some test assemblies and Creo behaves differently. ProE works as i expected.
Thanks.