Use `os.replace` where applicable (#793)

Use `os.replace` where applicable (#793)

When using
```py
os.remove(encodeFilename(filename))
os.rename(encodeFilename(temp_filename), encodeFilename(filename))
```
the `os.remove` need not be atomic and so can be executed arbitrarily compared to the immediately following rename call. It is better to use `os.replace` instead

Authored by: paulwrubel