Thankfully an email to the support guys at Github resolved the issue within a few hours. Still, I thought it might be a good idea to download my gists locally.
I can see all my gists as a JSON file online here:
https://api.github.com/users/MYUSERLOGIN/gists
Thus, I downloaded the file and thanks to the RJSONIO package I was able to clone all my gists locally with a few lines of R:
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