You have a knack for seeking out the more complicated aspects of Zbrush 
First of all, it’s important to understand the difference between standard Materials and Matcaps. Matcaps (the materials you see in the upper part of the material list) are materials (shaders) with the lighting information baked in. They are designed for quality surface feedback while sculpting, and quick preview without having to set up complicated lighting. Their lighting info will not update with changes to the scene lighting. When you assign a lightcap, you are altering the lighting information for a single material, not for the scene. If you want materials to interact with scene lighting, use the standard materials in the lower part of the list, and the original Lighting controls.
There are sometimes glitches with the Lightcap system, but I have no idea if that is what is happening here, or is just run of the mill user inexperience.
As far as restoring material settings, material changes should only save if you save your work as a .zpr project file (File> Save As). If you only save the tool (Tool> Save As ), then only your tool geometry is saved, and it will load into zbrush with the program defaults the next time you restart or initialize Zbrush.
If you have been saving material changes in a project file and want to reset them without resetting other aspects of the file, you can select the material you want to overwrite, then load the original material on top of it. (Material> Load). For windows, you should find all the mats in Zbrush4r7/ZData/Materials.