Activision Support here to offer some help. From the details in your post, it sounds like you are using the Elite console app. Please try using the Elite web site to manage your clan and see if you are successful there. If not, please know that the Elite team is investigating this issue accordingly but an ETA for resolution has not been set.
Regarding your missing MW3 Clan Level Emblems, please sign into our support site using your Elite or Call of Duty account then complete the following form https://support.activision.com/Clan_Emblem_Request_Form
If you have further questions or concerns, we can be reached via Facebook (Activision Assist) or Twitter (@ATVIAssist)