Hello Dimitrios,
Thank you for reaching out & I hope you are doing well.
I understand that you initiate the certificate rotation when your AKS cluster was stopped and now the actual start operation can't be accomplished.
While we usually suggest waiting for operations to gracefully terminate, we now have a preview option to abort long running operations or those that were initiated by accident, please check below Microsoft documentation and give that a try:
https://learn.microsoft.com/en-us/azure/aks/manage-abort-operations?tabs=azure-cli
The command that we should be interested in is:
az aks operation-abort --name myAKSCluster --resource-group myResourceGroup
Please "Accept the answer" if the information helped you. This will help us and others in the community as well. Feel free to reply with any other questions or concerns.
Hope this helps!