Rewired existing lights for a friend which had a 3 way switch installed to it and other leads to other lights, when I added a switch to one of the lights to remove it from the 3 way SW it worked fine but ended up removing power to the other lights downstream. What went wrong and how do I fix it?

You may have tied into a traveler on the 3 way wiring. Hard to see inside the wall but picture how a 3way is wired at the start. http://www.modmyrv.com/wp-content/gallery/mod-79-image-gallery/wiring-diagram-of-3-way-switches.jpg or http://ezdiyelectricity.com/images/wiringdiagrams/switches/3-way-switch-wiring-diagram.jpg