One of my devices dissappeared,
it's associated with my developer account but not my Apple ID.
How can I disable this phone?
See this link for info on resetting the device list associated w/your dev program account via the member center:
Note that you can't have a dev account without an apple ID, so at least one of your apple IDs is associated with your developer account.
Otherwise, you may want to contact AppleCare for assistance on a lost device.