Scoobster,
Obviously I am sure about that, otherwise I would be illegal to fly and so would my airline be as would my countries where I did my renewals!
My Licence is Belgian but I have held Dutch, Spanish an UK Class 1 certificates.
Only during your initial training do they want you to have a certificate from the country of licence issue, but this is ONLY until you finish your training. The reason for this is obvious, too many papers involved when processing your first pilots licence. The Netherlands, headed by a dreaded female doctor were the guilty party for implementing this rule. This is the rule you are referring to. Once you have your (f)ATPL/CPL, you are free to choose your JAA country to renew.