When you assign one variable to another, it’s not that both those variables are now linked by reference; you’re misunderstanding what “pass by reference” means here.
A variable holding an object does not “directly” hold an object. What it holds is a reference to an object. When you assign that reference from one variable to another, you’re making a copy of that reference. Now both variables hold a reference to an object. Modifying the object through that reference changes it for both variables holding a reference to that object.
When you assign a new value to one of the variables, you’re just modifying the value that variable holds. The variable now ceases to hold a reference to the object, and instead holds something else. The other variable still holds its reference to the original object, the assignment didn’t influence it at all.