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.
I have a UK-issued JAA PPL but I fly in the Netherlands and thus have to have recurrent training, exams etc. by Dutch-issued JAA instructors/examiners. The way I have always solved this so far is by letting the JAA instructor/examiner fill in the UK CAA forms (instead of the Dutch ones) and add a copy of his/her license to the paperwork, then send the lot to Gatwick. I would assume you would be able to do the same thing for that Spanish IR.
I do believe there is a domicile rule about having to have a JAA PPL issued by your home state..... There are rules on duration that govern domicile.
The only rule that I am aware of is that you can (but do not have to) transfer a JAA license to another JAA state if you live in that state for more than 180 days per year. For me that means that I'm quite happy to fly around on a UK-issued JAA PPL, but I can transfer it to the Dutch authorities if I choose, but not to e.g. the German authorities. However, once transferred to the Dutch, I cannot transfer it back to the UK CAA, unless I physically relocate to the UK.