There are a couple of threads I would direct you towards. They offer both justification for our analyzations and a bit of warning about what I would best describe as metagame thinking. Im not gonna be bothered by placing the links here, as I would prefer to continue with the discussion at hand.
This might be speculated on more appropriately if, say, Magus wielded the Doom Sickle in fighting Frog, but since you don't find the Doom Sickle until later, that's not a possibility
Anyways, as for the earlier statement regarding Magus not having access to the Doomsickle at the time of Frog's transformation; remember it is held in a Fortress held by Ozzie, a lieutenant of Magus. Ozzie does not wield a weapon as far as I can tell, and a scythe would be beyond him. Thus, I would imagine that Magus had access to the Sickle during the time he ruled the mystics. Why would Ozzie hide such a powerful weapon from his lord and master?
Perhaps Ozzie had stolen the Doomsickle from Magus when Magus deserted the Mystics and the palace was being absorbed into time, taking the big guns as his gravyboat was sinking? It would make sense for Magus's minions to loot and plunder as they leave; after all, they are all villains to begin with.
Just something for you to mull over for those stories of yours.
I've always found it funny how objects are just left around in treasure chests in various RPGs. Ozzie appeared to share that sense of humor, knowing no RPG adventurer would give up a treasure chest.
Trying to make sense of the Chaos is half the fun.