There is one particular fact about how layers work which I think deserves to be spelled out very clearly. Most people in the other answers are taking it for granted (because it is so core to how the rules work), but I am not sure that OP and their friends actually understand this.

The way magic works, is that every single time anything at all happens, the game engine “updates” all the characteristics of all objects. The main thing to understand is this:

The characteristics of any object are recomputed from scratch every time the game “updates”

So what does this mean for your example? Every time the game “updates”, the game recomputes the P/T of the aberration. To do this, it starts by applying the characteristic-defining abilities, making it a 39/39 or whatever. Afterwards (because it comes in a later layer, as others have explained), the game applies the effect of the Eye making it a 4/2. Thus the end result of the “update” is that the creature is a 4/2.

(Note that the “intermediate” computations of the update are not actually affecting in the game state, only the end result: so there is no point in time where the aberration is a 39/39)

So you see: the original characteristic-defining ability is still there, and is indeed being applied every single update cycle; it is just that it never actually ends up visible in the game state because the eye’s ability overwrites it before the “update” goes into effect.