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Azure VM SSH Certificate Thumbprint disappeared

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When I had created the Ubuntu VM back in October I followed the instructions provided below:

Azure How-to-Guide - SSH into Linux

I was able to successfully log into the VM via SSH for quite some time. This week I try logging in and am receiving a 'permission denied'. I've verified permissions of the SSH keys on my machine, then looked at the VM through the online management console and noticed that the SSH Thumbprint assigned to the VM was gone.

Now I've read through some of the forum and stackoverflow posts and tried uploading a new certificate by converting the existing PEM file into a CER file. Upload was successful via the online interface but it doesn't seem to refresh the VM thumbprint nor show up on the list of certificates via Cloud Services.

I then tried to use the CLI and found out that while my version (0.7.3) could upload .CER the certificate list was not updating there as well. I found the CLI had a newer version (0.7.4), but now the CLI only allows PFX so I convert PEM to PFX upload via CLI and check the certificate list.

Again the certificate that was uploaded doesn't show up on the list nor is the SSH Thumbprint updated on the VM.

Anyone have any ideas why this is happening or how I may be able to fix it? Is my only option to ditch this VM and recreate the whole thing?


UPDATE: The Operation Logs under Management Services show all the attempts to upload a certificate as Succeeded

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