So as said in the project, every time I reopen one of my projects the layers have all been flattened into the back round automatically. As you can guess this makes it nearly impossible to do anything. How to I stop Aseprite from doing this every time I open a project?
Make sure you save your work files to a format that supports layers, such as Aseprite’s native .aseprite format. If your images are PNG or some other format that doesn’t support layers, then Aseprite is forced to write out a flattened version. You can always export to these other formats when you need them.