@DTavs.exe  

 
It could be possible each full moon when the portal would open she’d sneak in for an hour or two and practice her magic during the time the mirror was mothballed in Canterlot (and later the Crystal Empire), which may be how she learned about the Elements being back in circulation again, who had them, Twilight becoming an alicorn, and finally the Princess Summit in the Crystal Empire.  
Then, once the events of the first movie happened and she finally felt regret for what she did, she became recalcitrant in going back, causing her to gradually become rusty in all things pone, which may be further complicated by the fact that the variant of Equestrian magic that began to permeate through the human world could be wholly different to the standard variety (and, if you want to get metaphysical, radiate through the body’s chakras in a different fashion) so by the time she finally went back, roughly about nine months time in the human world (I personally think the flow of time is disjointed between the universes seeing as Twilight’s friends in Equestria said she had come back practically almost immediately despite she had spent three days on the other side, and reinforced in Spring Breakdown as, based on the luminosity in the human world, the storm that battered the ship lasted overnight into the next morning, while in Equestria it appeared only a couple of hours had passed, though this also posits that since Equestrian magic began seeping into the human world, along with now always-on portal at CHS and the other wormholes around the world we now know exist since the events of Friendship Games, the time dilation appears to be weakening, and possibly in a couple more years the flow of time in both universes will finally synchronize. It all reminds me a lot of Digimon Adventure, where there was originally such a time dilation that the first time Taiichi came back, he actually ended up a few hours in the past relative real time, but when he returned to the Digital World somewhere in the realm of weeks to about a month has passed, and finally the actions of the Dark Masters and the lead-up to Adventure 02 showed that the dilation effect had largely ceased to be an issue due to the worlds becoming more intertwined in their co-dependent relationship) which could mean that she by then became so accustomed to being human, and along with the potential psychological effect of realizing everything good in her life seems to be in the human world (along with the theory of how magic works in the human world in relation to the human body I posited earlier), she managed to forget how to pone.

@Rpground  
Quite logic.

Apparently, Applejack was bitten by a magical spider when she was young.

@D_Tavs.exe 

Pfffffhaha! XD

@D_Tavs.exe  
Just what I was going to say. It would have been funnier if she was merely trying to figure earth ponies out.

@D_Tavs.exe  
This can be set much later. Hence “forgot”, not “isn’t aware”.

@D_Tavs.exe
 
Thanks, Captain Buzzkill

False, she remembers how to use magic, she used it on EqG 1 to steal the crown and she even teleports…

@PonyPon  
Well, she did spend years in the human world.

And forgot how to hoof as well, it seems.