Surely what they have done by allowing your medicals to follow through continuously is to expunge your temporary unfitness from the record.
I would write the medical section a letter stating this and ask them to ensure that all documentation relating to their error in medical findings is destroyed.
I would then copy the previous medical slip and the present one, and a copy of your letter with any subsequent correspondence and put them in your file of stuff which must never be thrown out.
Whatever they may say about the 'failure folder' the unbroken record looks better and you will not have to tick any box at any time which asks if you have ever failed a medical. You have the CAA certficates to prove that you have not.