I created a repository and then I renamed one of the files. The change is seen on github, but when I use nbviewer it’s not seen and I have the structure of the initial commit.
For example, the repo is here https://github.com/contactmodel/COVID19-Japan-Reff/tree/master/scripts and I renamed the script B to “B-MLE.ipynb”. Then, when I go to nbviewer: https://nbviewer.jupyter.org/github/contactmodel/COVID19-Japan-Reff/tree/master/scripts/ the filename is unchanged.
Something related is discussed here https://github.com/jupyter/nbviewer/issues/914 and it looks like there is a problem with github, not with nbviewer.