Editor: Texture painting with duplicate of a base-version texture
This might be related to #4736 (closed) .
When you are editing a mod, and instead of using the "added" version of the texture, you pick the "base"-version of a texture. If the same texture has been already added to the mod, the new texture ID resulting will be broken, rendered as seemingly random texture, visible by flicker of wrong textures during painting.
Editor-side of the issue could be solved by automatically choosing the added-version instead of the base, if such exists. I wonder if this is related to something deeper though.