I have a run of aluminum that is connected to a copper line from the panel. Is it better to replace the whole run or just have a electrician make the connections in the junction box correctly?

What is a "run of Aluminum" -A cable or the service lead to the panel? All SER wires to the house are aluminum.

I will always prefer that aluminum and copper cables are not mixed. They can be connected in an acceptable manner, but I would still recommend they are not mixed...