Alright I figured out a workaround. I had done the first step, but you also have to edit another file
-Rename the material's .json in the ..\Users\username\AppData\Roaming\Allegorithmic\Substance Alchemist\materials
-Edit the assetDatabase.json, Search and replace the old name with the new name. File is located in ..\Users\username\AppData\Roaming\Allegorithmic\Substance Alchemist\
Not the best, but it worked so far.