To upgrade from Spine 4.0 to 4.2, you must re-export your Spine projects using the 4.2 editor to ensure compatibility with the 4.2 runtimes. The 4.2 runtimes do not support files exported with 4.0 due to potential changes and new features introduced in the newer version. To avoid manually re-exporting each project, you can set up automated exports using scripts. This can be done using the Spine command line interface, which allows you to automate the export process for all your projects, saving time and effort.