After spending a day on the phone with GoDaddy, they informed me that they have an issue with the shared hosting and they can not update certificates on the various instances. According to them they had this issue on the past 3 weeks!
Of course nobody bothered to tell me and now the certificate is expired and I have no way of fixing it. I’m now in the process of moving everything to a separate hosting provider, starting from the repositories.
Of course now it will be a dedicated box, so the cost will not be the same. Any donation is of course accepted.