Can't access qualified import in incremental mode

Serialization/deserialization of qualified imports like `import c.d` seems to broken. Mypy gives a different error when using `-i` for this program:

```py
import b
b.c.d.f(1)  # "ModuleType" has no attribute "d" (only when using -i)
```

`b.py`:

```py
import c.d
```

`c/__init__.py` is empty.

`c/d.py`:
```py
def f() -> None: pass
```
