I had the same thing happen recently, also with A segments to ATH (on LH) that got swapped into J during a phone call for no apparent reason whatsoever. Bizarre.

I was able to call back and explain the situation to a new agent, who could see what happened and was able to reinstate things. I don't know if there was A space specifically still available or not, but there was definitely F space (the reinstated flights were booked into A as original).

Not sure if this experience is helpful to you or not, but I guess my advice is HUCA and be specific about how an agent changed the flight without your consent.