An upgrade to I class is just like any other (paid for by miles) upgrade. I have never heard of an FFP not giving credit for the original (paid) fare.

But yes, to be 101% sure a confirmation of the first experiences would be useful.

In any case, some nice Aegean Business flight reviews / trip reports would be great! Not just for the people flyign A3 regularly, but also to advertise their product somewhat (And hopefully land them some new customers)