Did anyone ever say you couldn't use the magic? It might need to be amended slightly, but you could still have a variation that for all intents and purposes is the same. (Tandavi has a similar magic, and I believe someone else is questing for something similar too.)
It sounds like you should have just talked to us about this, because if you had started a quest for a magic we would have never said "oh, sucks for you, even though you did this quest you can't have the magic".
But no, you wouldn't be able to have the pass back. It's unfortunate that you had to go on absent, but those interactions still happened for Rikyn IC, so it would be unfair to give you back the pass that made that development possible.
He only had to be invisible for September/October. If you full on broke that and made him visible, then your quest just failed. If you didn't break it, you could try turning it into Sparky and see what happens. (The worst is that if you just weren't active during those months and so didn't really contribute to the quest, then he might just make you go do something else). However, you're right, you would need a third magic slot. Like I said, you should have just talked to us. Having used up your active magic slots sort of puts you in a bind that I"m not sure how to solve. Either way, Sparky won't help you do anything if you have outstanding things owed to him. Then again, if you fail the quest, he probably won't be likely to help you anyways. Since the magic is darkxspark, he could just go to Moony and ask her.
Feel free to nudge me on Skype about this too if you want.
tl;dr : Get a third magic slot mutation and turn in the quest. Or tell Sparky you don't want to do it anymore (but he won't give you another one for a while, then), or ignore the Sparky quest and ask Moony instead (aka have Rikyn ask for the moon Goddess in response to what the RE said).