I've just transferred a server between Virtualmin Pro Instances, and was surprised to find that after the transfer the Virtualmin UI reported a self-signed SSL cert (actual cert is Comodo). On trying to view the cert and key in the UI, I got "file not found" errors. On checking the filesystem, the files were there, but zero length. I next tried a manual backuo to the target server, and a manual restore, with the same result. Finally, I manually extracted the file, and reset ownership as required, and all was well.
Not sure if I have done something wrong, or if this is a bug that needs reporting, but thought I should post the problem report, if only to help anyone else who hits this issue.