You have fallen foul of a rather silly piece of EASA legislation. You do not say which CAA has rejected your application, but it does sound rather like the UK CAA, in which case they will expect you to repeat the MEP Course and test so that you can apply within 6 months. The ATO you atended should have provided guidance on this matter and it should have been written in their Training Manual. You should contact the ATO for a solution. As there is no such time limit regarding the IR then that should not be affected. I don't understand why you would need a recomendation for training, only for an initial skill test.