Yes. Alchemist’s Genius grants “increased effect of flasks on you”, Modifiers to the effect of something “on you” always update dynamically when the modifier changes. Modifiers just to the “effect of something”, or to “something effect” (implicitly these mean- effect of something you create) are set at the time the “something” is created. This one is the former.
Basically there are two categories of effect modifiers – when an effect is created, the object creating it checks its stats that modify the effects it creates. For as long as that effect applies, the object it applies to can change the effect with its own modifiers to effects on it, which are dynamic. This difference is because often those are two different objects, and after being created the effect is independent of its creator, but attached to the thing it’s affecting. Thematically, it also makes more sense this way – logically shocking something and then swapping to a weapon that increases the effect of shocks you inflict shouldn’t change the shock you already inflicted, but getting shocked and then swapping to armour which reduces the effect of shock on you should work.