Spells are fairly powerful and their limitations are few, but thus far, one known limitation exists:

For reasons no one has yet been able to discern in-character, while you can do non-mass-preserving alchemy on a chunk of matter (e.g. turn an amount of iron atoms into the same amount of gold atoms), you cannot use mass-preserving alchemy on the exact same matter (e.g. turn the gold atoms back into iron atoms //plus// additional elements formed out of the excess electrons, neutrons and protons).

The reason this limitation exists is due to tighter [[:magic:Aether]] tie-in for non-mass-preserving alchemy. You can freely picture this as the atoms being manipulated being ‘captured’ by the Aether (picture a microscopic hug), preventing it from behaving like normal matter in the context of other spells.

This tie-in is irreversible in general. Applying a non-mass-preserving alchemical spell will forever lock that chunk of matter into non-mass-preserving mode. Having too much of this stuff around in general also makes it easier to ‘communicate’ with the Aether and, conversely, for it to ‘‘‘communicate’’’ with you.