You can edit the images, but as explained, Photoshop will wreck them. Other image editors may do better.
Did you export an atlas with PMA images? You can edit them, but Photoshop will show dark borders around the edges and wreck the PMA when you save.
Did you export an atlas with with bleed and without PMA? You can edit them, but Photoshop probably wrecks the colors of fully transparent pixels when you save, causing artifacts at runtime.
Did you export images that aren't in an atlas, like a PNG sequence? You can edit them just fine, they are normal images.