No, there is no way to prevent the over writing of the file. As mentioned, it is by design.
Also, no, you can not have 2 virtualhost entries for the same domain.
Last suggestion I can come up with is to navigate to:
Admin > Module Admin > Apache Admin > Override a Virtual Host > [Select Domain] > Custom Entry add:
Save and wait ~5 minutes and test again.
Also, no, you can not have 2 virtualhost entries for the same domain.
Last suggestion I can come up with is to navigate to:
Admin > Module Admin > Apache Admin > Override a Virtual Host > [Select Domain] > Custom Entry add:
Code:
ServerAlias *