If you tend to maintain multiple projects, and/or switch between multiple distinct program editing tasks, then you probably want to disable the Tools > Options > General > Remember Open Files and Projects Between Sessions option and instead manually open and close workspaces. The easiest way to keep track of these multiple workspaces will be to give them the same names as your project groups and/or projects, and store them in the same project directory where you store your projects and project group files (so they’re all conveniently in one place). Each time you start a new APN session, you’ll have to manually use File > Open Workspace to open the desired workspace. (This will open the associated project group, project(s), and files in one step, so there’s a decent payoff for the one manual step. Plus, if you keep all your workspaces in the same folder, it will always open to that folder by default, allowing you to just double-click the workspace’s .pnws file. When you close APN, it will ask if you want to save the modified files and the current project/project group file(s), and as long as you say Yes to that, it will automatically save the workspace back to the same workspace file that you opened. If you want to save it under a different name (to allow multiple workspaces for a single project), you can use the File > Save Workspace As option.
