@Mark Buckley I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue: Unable to connect to Azure MySQL flexible Server and when you logged in from Azure portal, a message popped up saying I have used up all my SKU credits despite not having done anything on the server.
Solution: As you mentioned you were able to resolve the issue by restarting from the portal.
If you have any other questions or are still running into more issues, please let me know. Thank you again for your time and patience throughout this issue.
Regards
Geetha