Changes to the default color swatches can be made by opening the swatch panel while no document pages are open and then after adding or subtracting a color quitting the program which makes it part of your preference file. Since the colors that you are dealing with were created for a document they will not be there when you close the document so they will have to be defined anew in the swatch panel using the process that I have just described.
After you have added default colors like this it would be a good idea to make a copy of your preference file for future occasions when you might have to reset your preferences but you don't want to lose your custom swatch panel.
The preference files can be found:
For Macintosh Users: With InDesign closed Launch a Finder Window in column view and click on your home folder. With the Option Key pressed choose Library from the Finder Go Menu. Within the Library folder find the folder called Preferences and within it will be found the folder Adobe InDesign which you should copy.
For Windows Users the file can be found at: C:\Users\[User Name]\AppData\Roaming\Adobe\InDesign\Version [#]