happy days
Further to my last, you may have an argument if you were not asked to sign a declaration when you accepted the FRI that you would pay it back gross under the new rules. This might be available if you accepted the FRI prior to those rules coming into force (in autumn 06). You might then be able to defer paying it back until your actual exit date, or even only in part, or not at all. You would need to spend a few quid to get some proper legal advice, and I can't guarantee you success. When the new rules came into force (by change to JSP 754), they were linked to a requirement that if you accepted an FRI, you would have to sign a declaration promising to pay it back gross before you were allowed to PVR. If you have not been asked to sign that declaration, you might just have a case.
As regards the tax, my best advice is that if and when you have documentary proof that you were paid the FRI net of tax, and you have paid it back gross, write to your tax office setting out your situation, include copies of the documents, and explain that, given the large sum that is likely to be involved, you naturally wish to reclaim the tax paid as soon as is resonably practical. Ask how you should go about this. HMRC has a duty to behave reasonably towards you as long as you have been completely open and honest, and in my experience they will do so. You may just receive another form to fill in first, but the hassle should be worth it in the end.
Regards
Ginseng