Do you mean you pack all the props into a single non-overlapped atlas uv layout? Why not pack these props all together before you start texturing? Also, what software are you currently using for each step?
You can automate mask rendering in substance designer for example, then use photoshop script to batch combine all textures from a folder into single texture, merge and bleed it. Unfortunately I can't give you exact steps, so if time spent on research and automation is worth it depends on how many textures you need to…
the problem is that painting all of them at the same time is a pain in the arse. I wrote a painter plugin that does it for me because I can but if you don't know how to do things like that then Dimwalker's suggestion is the best option. Set up an export preset that dumps a mask out along with the textures and then use…
Why bake one at a time ? just copy your hires and name as Hires_A and Hires_B (or split it accordingly) while low res objects as Low_A and Low_B and let Painter recognize the naming. Also Blender can bake several objects at once actually , one after another into same texture . You just need to uncheck "clear image" and set…