Just remember: Palette first, Map second. If you modify any palette, any map made with that palette will also change.
To keep map files, and palettes, as small as possible, very little information is kept in each.
A map file simply contains what palette(s) is used, and what number graphic is contained on each level of each hex, plus various other general settings, background graphic file, add-on graphic files, etc. The main thing is the palette information. Like hex 0101 has decorative Grass 2, no lake, no natural path, Heavy Woods Feature, Urban Road going North-South, no Upper path, no Detail, no wall and Elevation 2. But it does that strictly with numbers. So the data file hex 0101 might look like 5, 0, 0, 3, xx, 0, 0, etc. only in hexidecimal. Anyhow, say the 5 refers to the Decorative Grass 2. If you change the palette, or modify the palette, such that the 5th graphic is sand, or rocks, it will change what is displayed in that hex, and any others with that Terrain. So choosing a different palette, with an existing map, will almost definitely change things. And deleting one hex graphic in the palette will move every Terrain or whatever you're working with down as well, changing their numbers, and all the graphics associated with them.
Now, the palette save file is similar: For each number of each type of hex contents (say Terrain), it knows the hex text, modifiers, what graphic is used, etc. All but numbers and text, except that a filename for the graphic used, which must be in the palette's file structure. Keeping them all in a file structure makes copying a palette easy: just copy the palette folder, along with its .pal file and associated subfolders, to a new name, and you have a copy to modify. Under each palette subfolder (like \Terrain) are all of the graphics used by the palette.
If you only want to change what the graphics look like (you can draw better trees, etc. than I can), you can simply change the graphic used. "Woods, Heavy.gif" for example. You can do that without changing the palette at all; you're just changing what graphic is going to be used. It will still be called HVY WOODS, etc. It's best to do this after copying the Basic palette, so you can always go back to the standard ones if you like. If you want to change the text, to-hit mod, descriptions, etc. you'll have to do that within the palette tools in HMMap.
You can spend a BUNCH of time, working with the graphics and construction of palettes. I'd take it slow, make copies, work with them, change what you think you want, confirm it works right, etc. Things like Roads, Rivers and other paths become /extremely/ complex. You wouldn't believe the hours I've spent constructing the palettes, the graphics, and working with them. Change or add what you need to, leave the rest along, might be the best way to go.
And again, do ALL of this, within the program or when handling the files, as an ADMIN!
Again, hope this helps.
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