License Server issues

I have 2 sets of licenses that we purchase for two customer. One set was deployed and works. The second set was deployed and works. The problem is that they were deployed from the same license server. One of my trainees did not know any better and we are now delivering the systems. There is a designated license server for both sets of licenses. One is okay and the other has both sets of licenses in its License server. How do I remove the licenses that do not belong? These 2 sets of Snap Deploy will be in seperate locations and will never interact.