I've made some changes directly on the code located in the PythonAnywhere files. In this way, some of them are a little bit different from the reppository GitHub files. 
Assuming the PyhonAnywhere files are correct, what is the best way to 'copy' them and move to the GitHub?
Thank you!
If your PythonAnywhere project already connected to GitHub:

Run Bash console on PythonAnywhere
Move to directory with your repository
Make git push
Modifications PythonAnywhere -> GitHub