How to Merge Multiple Meshes and Bake All Textures into a Single Texture Without Breaking Materials?

Good evening. I created a room in Blender, and I want to merge all the objects into a single mesh and then combine all the textures into one texture atlas. However, when I join all the meshes using Ctrl + J, the materials get messed up, some of the meshes flip or behave strangely, and basically everything breaks. What is the proper way to merge all the meshes and bake all the textures into a single texture without ruining the model?