If I understand you correctly you're asking if when you add a "native" DUO account in your DUO Mobile app, if it will affect the existing 3rd party accounts you've integrated in the DUO Mobile app?
It should not.
You can have multiple accounts, both 3rd party and DUO-native in your DUO Mobile App.
The only time you would overwrite an existing account is when you enroll DUO from the same DUO account twice, for example if you've enrolled with your employer but go through the enrollment procedure again.
