Ryan Paule's Step-by-step Exploded Mesh Baking Guide
Duplicate both groups, then hide the original low poly and high poly groups. Now select the high and low corresponding objects and move them away. Do this with all objects until there is substantial distance between each object. Example, the “outer box” high and low will still both occupy the same world space.
Export the “exploded” low group as an fbx, then repeat with the “exploded” high group. After this, export your original low poly group with all the objects in the original world space as an fbx as well. Inside of Substance Painter start a new project using the “exploded” low poly fbx.
Bake the mesh maps using the “exploded” high poly fbx. Once the bake is complete, navigate to the Edit menu. Continue to navigate to the Project Configuration menu.
Press Select and choose the low poly fbx that is NOT “exploded” and press OK.
This process enables you to make adjusts to your low poly model and preserve the baked maps, assuming the uv layout has not changed. I hope this helps achieving the next clean bake. While one can always bake by mesh name, there is still a risk of the normals being affected by touching or intersecting geometry. So if you have complex models and/ or many close objects the “exploded” method can save you time and stress!