There is a form to use for the transfer of issuing countries.
Here is an example:
http://www.bazl.admin.ch/fachleute/s...NoKOn6A--&.pdf
and another one;
http://www.caa.co.uk/docs/33/SRG1136FF.pdf
I understand it can take a couple of months depending which JAA authorities you are dealing with...

My guess is you make the application with the authority that you want to issue the license.