Update wordpress to existing site issue

Hi, after I login to wordpress, in our dashboard we see this screen.

Since, I couldn’t update my wordpress from dashboard, what I did is I download the latest wordpress. Then I unzip it and manually upload wp-admin and wp-includes folder and the rest of the files except for wp-content folder:

https://www.findingsteve.net/v2/wp-content/uploads/2017/05/Capture2.jpg

This is because I still need to maintain my existing theme.

But, after I have done that, when I go to my site, it prompts to select the country which is the first step to setup my wordpress from ground.

So, now I have to undo my steps. May I know which files I should not overwrite in order for this update to point to my existing database and existing theme?

Regards,
Steve