When a file is copied out it does not have extra information regarding compression settings. It will then be run through the default compression, which sounds like what you’re seeing. If you want to keep the file exactly as-is, then you might want to put it into includes/ or somewhere else and load it completely dynamically.
That beind said – what materials render incorrectly after roundtrip? Our goal is that roundtrips in UnityGLTF work 100%, so if there’s something not working please open an issue in the UnityGLTF repo. Thanks!