Okay, I will write out this step in detail to help.
Open the png with gimp, go to Image toolbar and go to Scale Image. This will open up a prompt where you will see Width and Height and X Resolution and Y Resolution. Don't worry about the resolution stuff. The Width and Height is what we want to change. Hit the chain button so when you change Width, the height will change automatically. Set the Width from 2098 to 4096. When you apply this change, it should scale up the image. if the link isn't active, then the height won't update. If you are unsure what I am referring to, just enter the height to the Y value used in the atlas.txt.
Then go to File and press the button that says "Overwrite filename.png". You need to press this and it will update the PNG to the new scale. If option isn't there, then you want to export to png and change the name to match the original and delete the original.