OK, you appear to be referring to a situation where the pilot has say a UK issued JAA PPL but did a Spanish JAA IR.
The CAA may refuse to allow that IR to be added onto "their" PPL. A bizzare "join JAA and then stick a middle finger up it" restrictive practice worthy of the French, but I can see this being possible because the CAA "owns" "their" PPLs.
It would seem easier to get a Spanish PPL, while one is out there flying in the sunshine. Then the CAA is out of the picture completely. IIRC one cannot hold two different JAA PPLs but the Spanish one should be good for flying any EU-reg plane.
Another approach, with an N-reg, is an FAA PPL and any JAA IR. This should work for all IFR, worldwide. I don't believe one needs an FAA IR to fly an N-reg IFR.