You shouldn't have to be flattening layers to make JPG's. Just hit "SAVE AS" and select JPG. You don't need to use the specific Export options IMO If you do flatten layers (would it would technically do automatically when saving JPG's), make sure you DO NOT save them over your original files - otherwise you'll lose all your layer information and original file sizes/resolutions.
When I save JPG's in Clip Studio Paint/Manga Studio 5, for example, I SAVE the original file, then change the image resolution to my required size. I hit Export, then JPG, then I save the JPG's in a folder made specifically for JPG's. Then I close out of the file, without saving over it with the compressed layers. This way I get both my JPG and can keep the original high-res file with the layer info intact. Same goes for Photoshop.