I'm noticing that now when I remove a turret that has leveled, it leaves a ghost box where the turret was.

Also, my construction robots won't replace turrets that leveled up.

Not sure about ghost box? Its just another entity copied from base entities and adjusted.
Wont replace? Do you have the right ranked turret available to them. I might need to change the ghosts to base entities if killed, that probably makes sense

The hit box issue might be a conflict with the Turret Shield mod. I just know it wasn't doing that by itself (or even now with un-leveled turrets).

No, that would be a bit difficult, since I can't craft ranked turrets. But usually when you replace a ghost turret they keep their kills.

Ranked turrets will drop base turrets now only. kills won't be retained as that entity is dead now anyway.
when picked up the kill count has been lost however I have made an option to allow recording actual kill counts but this will mean each turret will be stacked with other turrets with the same kill count so it could be messy

Honestly, I think a better option would be to change the ghost to be the "base turret". That way we can just build a new one and a robot will plop it in.