Assigning a dict over a dotted key renders a stale parent. prefix

Similar flavour to #513, but this one introduces an unwanted header where that one only failed to reorder the document.  Maybe they will turn out to have the same fix.
```python
import tomlkit

doc = tomlkit.loads("fruit.apple = true\n")
doc["fruit"] = {"a": 1}

print(tomlkit.dumps(doc))
```
result
```
[fruit]
fruit.a = 1
```
which has too many fruit.