Hi, thank you so much for the detailed report — your diagnosis was exactly right.
I reproduced it on Godot 4.3 and 4.7.2: the shader colors (color1, color2, tint, main_color, bg_color) were stored as Color on plain vec4 uniforms, so Material.duplicate() dropped them to the shader defaults, and it even cleared them on the shared original material. It affected every effect in the pack, not just Slash_fire.
Version 1.1.1 is now up on itch.io. All scenes store these values as Vector4, and I added checks for this to my build tests (tuning back and forth, duplication, and save/reload). Your inherited scene may still hold the default values from before; re-creating it from the new Slash_fire.tscn (or restoring the values as you did) fixes it.
Thanks again for taking the time to dig into this!