I had this problem develop over the last few months to my LIII and SM-Y2D. I asked the Ernie Ball Reps at NAMM what to do and they said DO NOT have the frets filed because once humidified the frets will be too short. It was recommended that I buy case humidifiers and give it some time.
I bought the Oasis Guitar Humidifier Plus+ (because I live in the desert) for each case, an Oasis Hygrometer, and a small room humidifier on Amazon for $33.00 I found out the humidity in my house is very low at 30% and needs to be 45-50%. I didn't realize that electric guitars are susceptible to dryness much like acoustic guitars. I treated the fretboards with Wonder Wipes, fresh strings, and cased them with the humidifiers (and I always keep them cased when not playing).
In two weeks time, my guitars have just about recovered back to their original state. The last few frets on each guitar need a little more time. I moved the Oasis Humidifier from behind the headstock to the open area in the case next to the 22nd fret. I'm monitoring them everyday and should be in good playing shape soon.
The room humidifier allows the case humidifiers to not have to "work" or dry out so fast. Plus, a bonus I didn't think of is that I've never slept better! My house feels like the acoustic room in Guitar Center.