When we replace exiling Obzedat with it second ability to putting it in command zone, will it still return in it's controller next upkeep? Need confirmation in CR.

Yes, Obzedat's delayed trigger will return it to the battlefield from the command zone at the beginning of that player's next upkeep.

Thanks to the Commander replacement effect, Obzedat's triggered ability puts Obzedat into the command zone. This causes it to become a new object–and the ability knows which object it is because it's what created it. The delayed trigger the ability then sets up tells you to later do something else with “it”, meaning “the object I was doing things with earlier”. And that's the object it created: the Obzedat currently sitting in the command zone.

Daniel Kitachewsky
L4, Paris, France
Rules NetRep