I just remembered something else.
There is an option to save a template file which when executed saves a file that is used when you first start C4D. Â After that it will use your new.c4d file.Â
To remove this file, open C4D preferences (Edit > Preferences), hit the button at the bottom to open the preferences folder. Â In the prefs folder you should find a file called template.c4d. Delete this. Then close and reopen C4D. It should now use your new.c4d on every file, including the first one.
If that doesn’t do it, or that template file doesn’t exist, I give up.