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I hit the same issue ~2 weeks ago whenever I was upgrading image from c800-universalk9-mz.SPA.153-3.M7.bin to c800-universalk9-mz.SPA.154-3.M7.bin.
After reboot router lost all rsa keys and flash drive had file systems errors.
restore certificate bundle from pksh12 file I exported rsa keys, certificate and intermediate certificate before router upgrade.
I didn't take so much time except I had to go to remote site where router is.
Have not seen this issue per se, but i know that in some versions, the SUDI key that was automatically generated was being used for the SSH key. This is instead of the default RSA keypair generated for SSH ( because SUDI key is generated earlier). You may have to to change the SSH config to use the new key:
ip ssh rsa keypair-name keypair-name
It is possible the SUDI feature may have taken over your SSH key and caused the default RSA keys to be deleted since it was not being used. Might be worth a look to see if the issue can be reproduced on a non-production device.
Thanks alot, this was exactly what I was looking for.
Will try to re-create it in the lab and post an update later today.
Have been unable to recreate the problem...
But have upgraded several more, and after doing a "no archive" before the upgrade, all the upgrades have been working.
So thanks alot for finding it for me.