I support changing one of them. Having two very different things both be called "Alchemy" really is silly and easy to confuse.
I know that battlers are set in their ways, but honestly, alchemy from reading books just doesn't make sense and never has to me. I get that it is based on how many games link intelligence to magic... but Alchemy should be reserved for the zombie place, considering that is actually called the Alchemist's Alchove. I am fine with keeping the abbreviation as AP though, as suggested. Maybe Academy Points? Since it is linked to intelligence and learning.
I always thought the alchemy from alchemy points came from how scrolls were crafted - combining ingredients in the shrine to form the spells.
I'm never certain why scroll creation is referred to as alchemy. I suppose it's the same mechanism (in general) as what happens at the Alchemist's, but I feel if you buy ingredients at the magic store and make magic scrolls from them, the term for the process should be more magic-related.
Regardless, there is confusion and I would love a little clarity/difference, however that ends up happening.