Just quickly, how many atlases do you have?
If its only a few you can just include both, texturepacker can export multiple resolutions easily if I remember rightly.
Then depending on the profile of the context you created you can load the correct texture.
(Texture Too Big: if either the width or the height parameter is greater than 2048 for baseline and baseline constrained profile or if either the width or the height parameter is greater than 4096 for profile baseline extended and above.)
So if you profile is baseline extended and above you can use 4096, otherwise use 2048.
If you don't want to include both you can downsample on the cpu before and and transform the values in the xml file fairly easily to convert from 4096 -> 2048.
But it does depend on how many atlases you have.
You do also want to consider the size of things on screen, there is no benefit to massive textures if they are always displayed at a lower resolution anyway.
Quick rundown of the profiles from lowest to highest:
Baseline Constrained -> Baseline -> Baseline Extended ->
Standard Constrained -> Standard -> Standard Extended ->