Use Them and Replace Them
Cyphers are always single-use effects and are used up when you activate them. In other words, unlike an ability from your type or focus that you can use whenever you want, a cypher is something you use once and then it's gone. They're a game mechanic designed so that you discover them frequently, use them when you need them, and find more to replace them.
Usually, you'll find new cyphers at least once each game session, so don't be afraid to use the ones you have—you'll get more soon.