I linked my Github account to C9 and cloned a private repository. Then I made some changes to the files and uploaded a couple of folders through the IDE, and in the end used git push in the terminal in C9. This caused the changes in the files to update, but the new folders that I had uploaded and the files in them are not there.
You told us that:
and in the end used git push in the terminal in C9. This caused the changes in the files to update, but the new folders that I had uploaded and the files in them are not there.
You may have done a git push to the repository, but this would not send any files/folders new or old which were not staged. To see where you stand locally, type git status from the Git console. My guess is that you will see the folders which never seemed to make it to the repository under the "Changes not staged for commit" section. To fix this, you can do git add on the files and folders, and then push again.