You need to find out if someone else was promoted to leader when this happened and request that they use the ghost app to re-promote you to leader - failing that you could try to contact Activision through twitter to see if they can help in any way or hope that one of the Activision assistants read this post and try to resolve it for you, sorry I couldn't give any more help.
Who does it show as commander of the clan right now? Also, does the commander appear the same to everyone in your clan? We are aware of some players experiencing functionality issue with the app at the moment and Beachhead is currently working on it. You can find more updates here Beachhead Studio. In the mean time, please relink your game account to your Call of Duty account and let us know if that helps.