Good question and as a Phoenix wallet user, I'm happy to answer. Your LN channel backup is actually replaced with the ln channel state that Phoenix has every time you open the app. When you enter your seed phrase, you get your LN channel state backup from the Phoenix servers.

This is the only wallet I've seen do it this way. Breez for example encourages you to set automatic backups to google cloud and blixt does the same thing.

So be aware of this.