Although I have answered this point at SharePoint 2016 web application could not be extended I will add here additional info by answering your specific questions one by one.
Will removing extend web application affect the content database?
No, The main Web Application and the extended one will share the same Content Database, and removing the extended web application will not affect the content database.
Why extended web applications are not listed in the Manage web application page in central administration?
It's normal behavior, only the main web applications will be listed on this page.
How to remove extend web application in SharePoint 2016?
To unextend web application SharePoint 2016, you should follow the below steps:
- Open Central Administration > Application Management > Manage Web Application.
- In the Manage Web Application, the extended web applications will not be listed, only the main web application will be listed.
Select the main web application, from the above ribbon, click on "
Delete" > Remove SharePoint from IIS Web Site.
Select Yes, if you would like to remove the extended web application with the IIS site > then click Ok.
For more details, Please check Extend Web Application SharePoint 2016