How to preserve changes to native GitHub repo between builds

Hi All,   For a native mobile project I'm working on we commit some custom stuff to the react native project on GitHub; changes to the podfile being the most critical, but there are also some xml changes on android. Without these changes the build takes too long and the build process times out on AppCenter.   The problem is that every time I build a new app via the UI builder in studio Pro it overrides all the custom changes on GitHub.   Is there a way to prevent this from happening?
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