Member references in method bodies are not always updated.

[Col-E]

This seems to be a edge-case. I've only experienced it when the name of the member being referenced shares the name with a member that does not belong in the jar.

One such example would be:

public void test() { println("Hello!"); }
public void println(String s){ System.out.println(s); }
public void println(String f, String s){ System.out.printf(f + s); }

This becomes:

public void a() { println("Hello!"); }
public void b(String s){ System.out.println(s); }
public void c(String f, String s){ System.out.printf(f + s); }

The method declarations are updated fine, but the references to them are not. Does not occur if the methods are named something else unique.