Double click on the swatch that you would like to change to enter the
Pattern Options window.
direct selection tool select all the elements in your pattern.
Double click the color swatch box for your
fill and enter the color you would like for your new swatch.
If you find that the color is a shade of grey instead of what you have chosen, navigate to the
Color window and click the menu options icon on the right hand side (it will look like three lines stacked vertically.)
Select one of the four color options (in this case I've chosen CMYK) and the color you have chose will now be reflected in your pattern.
Save your pattern
as a copy and rename it to save it to your pattern swatches in the