The theory that Amara will turn out to be Cyrus' mother is one I thought of as well when I read the synopsis for that episode. Since we've got two options for Amara's presence in the episode (she's either in Cyrus' flashback or restored from being Jafar's staff), I'd like to think that she's part of Cyrus' backstory. Since we've already seen one example of a human turning into a genie to save someone they love from death with the Knave and Alice (yes, I know Anastasia's his true love, but he does love Alice as a friend), it makes sense that Cyrus and his brothers became the 3 genies when they tried (we hope and presume successfully) to save their mother. If Amara is their mother, then we can assume that she has been searching for the 3 genies in hopes of saving her sons and ending their enslavement.
Of course, we could also see Amara as a sorcerer who tricks Cyrus and his brothers into becoming genies so she can perform the still-undefined magic-changing spell that Jafar's been after all season. I like the Amara is Cyrus' mother theory better, myself.
That could happen. She did have the master plan of using the 3 genies to change the laws of magic. Or someone could undo the spell on Jafar's staff (In present time), making Amara back into a human again.
I think this twist makes the "how many ginies are there" matter much clearer: there are definitely more than three (Magic Mirror), but Amara was specifically looking for those three because they're her children. Makes sense.