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If I understand you correctly, those are the Color Map save/load buttons.  These load/save an individual color mapping.  The Project load/save buttons save an entire project (src image, palette, ALL color mappings, etc).  

The idea is to provide a method for sharing individual color mappings between projects.   For example, you might set up a general purpose mapping from say the Sega Master System palette to the NES palette.  You could then save just this mapping and reload it into whatever projects you might want to use it for.

If you open the text files in notepad (or the text editor of your choice) you should see some difference in the contents between a Project save and a Color Map save.  If not, let me know!  :)

BTW was just testing this to make sure before answering your question and noticed that the load/save dialogues for an individual color mapping refer to the mappings as a 'Color Swap Set' when it should call it a 'Color Map' to match the rest of the GUI.   Sorry for any confusion that might have caused.  Internally the code calls maps 'color swap sets' for whatever reason and it looks like I accidentally let some of that language slip into the GUI.  Will try and remember to change the dialogue titles the next time I roll a build.

Thanks for the kind words, so glad to hear you find the tool useful!