You could write a script to update the FK's for you.. check out this blog: http://multunus.com/2011/03/how-to-easily-merge-two-identical-mysql-databases/
They have a clever script to use the information_schema tables to get the "id" columns:
SET @db:='id_new';
select @max_id:=max(AUTO_INCREMENT) from information_schema.tables;
select concat('update ',table_name,' set ', column_name,' = ',column_name,'+',@max_id,' ; ') from information_schema.columns where table_schema=@db and column_name like '%id' into outfile 'update_ids.sql';
use id_new
source update_ids.sql;