I dont think it is odd that one part dies and another part lives. That is the natural behaviour of junipers in the forests around me. If you look online for really mature old juniper bonsais you will find that the deadwood left behing is a sought after feature. Even to the extent that we selectevly kill branches to make "jin", deadwood.
However I find it odd that it is showing it now. The dieoff happens in winter and show itself in early summer. I dont know your climate, but were I am in Western Sweden similar to usda zone 7 it is visible before end of may.
Also, on a such young tree it is not wanted and it is possible to avoid by good care and protecting the tree in winter.
Your dead branches will not recover. But with good care the branches remaining will live.