I solved it by myself now. Here is the solution, if somebody has the same issue in the future:
I opened the Substance Graph Instance of the Material which resets itself everytime. I deactivated every single output slot of it. Every time I ejected an output, the input graph window closed itself on me. But the unchecked Box remained unchecked. I repeated it for every slot it had. Then I activated every output again. Once I had the Textures created inside the same folder of the graph instance (which is not preferred by our pipeline) I moved them to the textures folder, saved everything. And it works now. The Textures wont get reset anymore.
I dont know if it was a *.uasset error of unreal, since the files were saved before… Or it is a problem with paths from the Graph Instance…
Since the beginning, we separated the ‘Instance Factory’ together with the ‘Substance Input Graphs’ and moved the created Textures to its own folder.
Assets → Materials → Substance (<- IF & SG)
Assets → Textures (<- Textures)
While we don’t want to have any issues with that in the future, we won’t use substance graphs inside unreal anymore and use the player to create the desired outputs, to create a ‘baked down’ Material.