I'll go with the people who say no. As long as people clear duties and it is valid in the eyes of SE, it shouldn't matter if it is synced or unsynced.

As far as commendations go, don't worry too much about it. I earn my commendations and I don't really care how much I get because all I care about are helping others, clearing the instances, and getting rewarded (especially the Adventurer in Need Bonuses as tank. *wink)