Yeah I've noticed it too missing in my link manager on my main. I went back on my Kinesis to make sure it was linked with my main. After looking and saw that it is still linked, I went back on my main to open up link manager and it's there now. Pretty much the same thing you're experiencing, I didn't pay attention to see if the link was still being applied when it wasn't present my link manager though.
@ielmo: I have a Beast Tamer link skill somehow at Level 1. I do not have a Beast Tamer created in my world, and to my knowledge, link skills do not transfer along with the character they were linked to during a World Transfer.