Unable to remove domains from old license

I am trying to remove an old directory containing 2 domains from an old license to sync them with our new license, however I am getting - 

"The following domains have users and cannot be removed. You need to remove all users with these email domains before you can remove these domains."

I have been through the users and directory users tabs and removed every one I was able to, we still have ~1000 that cannot be removed as the box next to them is greyed out.

Any advice would be greatly appreciated!

James