Yes an avenue of appeal does exist.
Here are the relevent JAR'sJAR-FCL 3.045 Special Circumstances
Date: December 1, 2000
(See AMC FCL 3.045)
(a) It is recognised that the provisions of all parts of JAR-FCL will not cover every possible situation. Where the application of JAR-FCL would have anomalous consequences, or where the development of new training or testing concepts would not comply with the requirements, an applicant may ask the Authority concerned for an exemption. An exemption may be granted only if it can be shown that the exemption will ensure or lead to at least an equivalent level of safety.
(b) Exemptions are divided into short term exemptions and long term exemptions (more than 6 months). The granting of a long term exemption may only be undertaken in agreement with the JAA FCL Committee.
For medical variation and review policy see JAR-FCL 3.125.
JAR-FCL 3.125 Variation and Review Policy
Date: December 1, 2000
(a) AMS Review. If the medical requirements prescribed in JAR-FCL Part 3 (Medical) for a particular licence are not fully met by an applicant the appropriate medical certificate shall not be issued, revalidated or renewed by the AMC or AME but the decision shall be referred to the Authority. If there are provisions in JAR-FCL Part 3 (Medical) that the individual under certain conditions (as indicated by the use of should or may) can be considered fit, a variation may be granted by the Authority. The AMS may issue, revalidate or renew a medical certificate after due consideration has been given to the requirements, acceptable means of compliance and guidance material and to:
(1) the medical deficiency in relation to the operating environment;
(2) the ability, skill and experience of the applicant in the relevant operating environment;
(3) a medical flight test, if appropriate; and
(4) the requirement for application of any limitations, conditions or variations to the medical certificate and licence.
Where the issue of a certificate will require more than one limitation, condition or variation, the additive and interactive effects upon flight safety must be considered by the AMS before a certificate can be issued.
(b) Secondary review. Each Authority will constitute a secondary review procedure, with independent medical advisers, experienced in the practice of aviation medicine, to consider and evaluate contentious cases.
I don't know of anyone who has asked for such a review.
Clearly under 3.045 (special circumstances) the JAR says "Where the application of JAR-FCL would have anomalous consequences".
Obviously an anomalous consequence would be that you could qualify for a FAA 1st class medical and with appropriate licences fly in and out and all around JAA airspace to your hearts content in an N reg aircraft.
It also states "An exemption may be granted only if it can be shown that the exemption will ensure or lead to at least an equivalent level of safety."
No problem getting such evidence. Visit the FAA website and search for it. All FAA studies and findings are public record and you can order them for a small fee. If the FAA previously had a restriction regarding your medical problem they would not have removed it unless they had conducted a study of it and demontrated that safety would not be compromised. Get a copy of the relevant publication and submit it with your request for a review.
Good luck