Manual migration resets theme to first install state

After I copied files and database to my local WAMP server the theme settings were reset to seems to be like the first install state. I could see old settings (like custom styling etc) in the database (“options” table) after I import old database but before I try to use the site. After the first use of the site the theme gets reset and all custom settings disappear.

We are changing our site’s maintenance and development process to automate deployments and use GIT versioning system so this is important for us to find the way to transfer copies of working website to different hosts. How could we do that?

Thanks for the answer Simion,
However, we do not have access to the production server administration panel as server updates are done by GIT and other cli deployment tools, and because of Continuous Integration those changes are pushed to the live server very frequently, therefor we can not use the Duplicator plugin.
In fact we have no issues with moving code and database from server to server except the issue with the Newspaper theme that I mentioned before. And to resolve it I would like to know what function is clearing the theme’s custom settings so maybe I could disable it.