This is similar to https://issues.dlang.org/show_bug.cgi?id=2417.

Test-case:

base.d:
```
import derived;

class Base
{
    protected void func() { }
}

void main()
{
    auto derived = new Derived;
    derived.func();
}
```

derived.d:
```
import base;

class Derived : Base
{
    protected override void func() { }
}
```

~/dev/d master * $ dmd -run base.d
base.d(11): Deprecation: derived.Derived.func is not visible from module base
base.d(11): Error: class `derived.Derived` member func is not accessible


The fix is to change:
auto derived = new Derived;

to:
Base derived = new Derived;

But I don't see why the compiler can't access it in the first case, it's still a virtual call after all..