I can't provide a full explanation here, especially since this isn't really something I have really noticed myself.

But let me address one thing at least:

All CC3+ maps have a setting that determine if effects are on or off on load, you'll find this in the :CC2RESMODE: dialog. This is a per map setting. If this is off, the map is loaded with effects off, even if it was turned on inside CC3+ previously. You can override this behavior from Tools -> Options

Now, while you experience that effects randomly turns off, I don't know, but i suspect it could be due to loading a file that sets this value. There are lots of cases where CC3+ loads map files, for example, symbol catalogs are actually just map files with a different extension, and drawing tool previews in the symbol catalog window can also be map files. I am suspecting that maybe the value is incorrectly set when something like this is loaded.

You can just rename it. The maps doesn't refer back to the .fsc file even if you've inserted symbols from it. As long as you don't rename any of the underlying art (png) files, or the folder/path they're in, you're fine.

What Sue says about using the PNG instead of the symbol id right, but you don't need to go around hunting for the png, simply place the symbol you are going to modify, then :CC2EXPLODE: it, that will turn it back into it's individual parts, for most png symbols that will be the image it is made from and nothing more.

But, you also said something about sheets. Do note that symbols DO NOT contain any sheets. When you define a symbol, sheet information is lost. So when creating a symbol, you should always place everything on the same sheet and just rearrange things with the front/back buttons. This ensures that ordering is proper.

(A symbol CAN go to different sheets if you use the line style to sheet options, but this splits it into several symbols on placement.)

Commercial fonts, assuming you actually own the license to said font, allows you to produce documents using it, so exploding it should be completely fine, as you are not making the font available to others in any way by doing that. So I have no problem with that.

Well, the atlas is absolutely non-commercial, neither me, nor the contributors earn anything from it. The big problem with non-commercial though is that it is poorly defined, and a lot of licenses have a slightly different take on what that actually means. Technically, this forum IS a commercial entity, because it is connected to ProFantasy's business, but most licenses are still happy with end users posting things made with non-commercial usage licenses in such forums to show off their own work as long as they don't personally earn money from it. But for that atlas itself, I don't seeany problem with using such fonts as long as their license doesn't explicitly forbid it.

Nice work so far.

I was looking at your .fcw files, and I noticed that some of the colors around your mountain regions were a very bright pink.  I am suspecting this is not intentional and is due to you having an non-default palette installed. If this is the case, I recommend attaching the palette to the drawing so it follows the file instead of having it in your CC3+ data directory as a separate file affecting all maps. You can attach the palette from the :CC2PRESETS: dialog.