I'm not sure about this, but there are two things which came to my mind:
Maybe you changed not only the color but also the opacity to black. In that case the particles will stay invisible:
2.) The effects Composite Mode:
If the current composite mode of that particle effect has been set to 'Add', black particles will disappear. (That is because black is 0 which adds nothing to the background layer.)
If this doesn't help, feel free to post more details or (if that is possible) upload the project file somewhere, so I can take a look.