Hi Krishna,
I do not have that version of PowerDesigner and tested your scenario with PDes 16.5.4.4 (SP04, PL04). I cannot reproduce your issue.
I created a simple logical model, go to Tools, Generate Physical Data Model targeting DB2 UDB 9.0. Then in the PDM, created an Owner on the table. Then went back into the LDM, added an attribute, regenerate the model with the Preserve modifications turned on. I made no changes in the Merge Dialog and my owner information was preserved in the PDM.
I would either try again or look to see if you can upgrade.
Sorry, wish I had a more direct answer.
-Matt C.