baking and lightmapping with dynamic level building

Greetings, I've been building different levels in one scene using only a few prefabs (with multiple objects per prefab) and instantiating them onto their rightfull place.

Now i've recently started looking at baking a scene, which ofcourse will be hard to do so when you have an empty scene. So i put the prefabs into my scene, bake the lights, and remove them afterwords.

When I run the game and it works perfectly ( as long as the prefabs instantiate on exactly the same places). But the're multiple level setups with a few changes into prefabs positioning, prefab use etc.

After some research I learned you can lightmap a scene, store the lightmaps (and probes) into the resource assets and set them correctly using code.

So now i have one scene, 3 different level setups and 3 folders with the lightmap assigned to that certain level. And it worked pretty good a long as it would be only 1 lightmap.

The problem is that 1 lightmap won't do much good for creating a good image, so i need more of them. But when i assign 2 or more lightmaps while instantiating a level, they always get mixed up by the meshrenderers.

I've tried lightmapping per prefab, but each bake responds differently and overwrites lightmap 1 when baking lightmap 2 for a different prefab.

Any help or ideas would be great! Thanks in Advance