Are you sure that you're getting the duplicate spell then? Because it should be working if you start the game as a Wizard. Try setting the Element to Water and see if it shows up in the Hydrophist school.
I know I have made a duplicate skill or two back when I was messing around with skills, such as a modified Lava Core for my "Painting the World Red" thread, and maybe for my Purchasable Skillbooks mod. If you want the skill to truly replace the other, you will need to have the normal Skillbook point to your new skill as well.
Changing the element to water in the duplicated spell gives this message "Changing Equipment dropped level(s) of Hydrosophist. Because of that you unlearned Flare".
So that had an effect. Changing descriptions or action points doesn't however, in that case the game seem to read from the spell that i've duplicated from. weird. Did you manage to change the description and in game name of the skill without starting to mess with the localization folder in the main game?
