Fractal Capacitor (Infused) Skin change
If you you put the flower on top of the capacitor you should be ok. It should register in the mystic forge, and should be able to be used in the recipe to ascend it. You will loose the flower skin but the capacitor skin will be back.
Easy way to check. Unequip it and go to the mystic forge, if it can be put in it will work.
As I’ve heard, once transmuted, you can’t upgrade it anymore. Only transmute it after you’re finished upgrading it.
So what is the right answer? Can I put the flower and then mystic forge it?
THIS IS THE RIGHT ANSWER. Wiki says that if you reskin ascended fractal capacitor mystic forge will register it as capacitor not as flower and after upgrading it will lose flower skin and become beta or whatever your next stage is.