"Secondary" can mean many things. The most common view is that a person in a serious relationship starts to see someone else. That new relationship is usually labeled secondary. But that says nothing about the feelings in the relationship. It says more about who sleeps with whom by default or where a person tends to spend the night.
But secondary can mean many other things. It may just mean that it was the next relationship after the first relationship. Or it can mean that it is a relationship with less value than the primary one. Or it can mean that it is a relationship with more of a specific focus (like BDSM partner). Or it can mean the relationship is a distant one in which it is tougher to feel close.
I would suggest you ask the person saying it if it sounds confusing at all to see how they see it.