Merging Projects

Hello!

We have a big problem that after months of searching and testing we can't find a working solution for. In desperation, we're reaching out to see if you might be able to help share your expertise.

Our team is working on an app. Each level is being created as its own project and then merged into the main. This has a ton of benefits from a workflow perspective...

...except that we can't merge these projects into the main without big issues. Prefabs will be replaced. Materials will be swamped. Fire and brimstone, cats and dogs, etc. It is bad.

We now rename all materials, prefabs, and meshes in the project to be added, export to a package, and import this in. We also put all of these in a sub-folder so they don't interact with other items. Yet, even with all of this, things don't transfer over smoothly.

Example: We imported in a new package and it all worked great, except for the water and a series of prefab rocks. Both had been renamed in full. But they appear as other rocks and water. So our carefully crafted piece is busted, possibly breaking other items in our project too. Yay.

Of all areas we didn't expect this to be the challenge. Any ideas or suggestions? Thank you so much!

Side questions:

Is there a way to delete Unity's metadata cache? Would this help?

We rename all meshes we can, but some aren't able to be renamed (gray). Why?

Is there a way to break the original prefab connection fully and mass apply as a prefab? In the rock example, is it that these were based on another prefab originally that is the issue.