Wolverinecm is correct. Here is the quote from the Clan Operations FAQ http://support.activision.com/articles/en_US/FAQ/Clan-Operations--FAQ/?q=clan+op eration&l=en_US&c=Platform%3AElite&fs=Search&pn=1
Your Clan stats count toward the last team you were on during enlistment.
- Joining another Clan during a Clan Operation
If you were enlisted in Clan A but joined Clan B in the middle of a Clan Operation, only your score with Clan A will count.
- Leaving a Clan during a Clan Operation but not joining a new Clan
If you were in enlisted in Clan A during a Clan Operation but left Clan A before the end of an Operation and didn't join a new Clan, your score will count towards Clan A.