Did Latisse Fade my Permanent Eyeliner?

Latisse should not fade your permanent eyeliner.  It simply makes your eyelashes grow and get darker. 

There is NO physical or physiologic way in which the prescribed application of Latisse can fade or erase eyelash tattoos. Latisse stimulates eyelash follicles to stay longer in the growth phase, It has no ability to bring about mobilization of tattoo dye.

Latisse will have no effect on permanent eyeliner. One of the problems with "permanent" eyeliner is that it's not really permanent and will fade over time anyway.

One of the effects of Latisse is to activate the melanocytes, causing them to increase pigmentation. Latisse also causes a prolongation of the anagen (growth) phase of the hair cycle. These two affects cause eyelashes to grow darker and longer respectively. There is no physiologic reason that they would fade eyeliner. Instead, I would question what chemical was used in the production of your "permanent" eyeliner.