I'm working with the 2D Renderer and use URP Sprite-Lit and Sprite-Unlit shaders in shadergraph. Until Unity version 2020.3.0, there was an output called Sprite Color. Now it is divided into Base Color and Alpha. When updating the project, my shaders were still using that apparently deprecated output and were working until I opened them, chose a different Material (in the Graph Settings --> Universal --> Material property) and then selected the same Material it had originally. That change updated Fragment box, showing the Base Color and Alpha outputs.