Mac OS Mojave Terminal Resetting to Default Theme
Setting the default profile does not mean that it will launch with the new window on startup. You need to set that in the General preference on startup, open: New window with profile: [YourProfile]


  is there a config file where I can change the theme manually?


Yes, you can edit the ~/Library/Preferences/com.apple.Terminal.plist in XCode (it's a binary plist file so while you can view the file in a text editor you don't want to save it as ASCII text).

You may actually want to delete this file though. After deleting it, when you launch Terminal it should be recreated with all the system defaults. That way they are there. You may have gone overboard with deleting everything.