I do not think it's possible to lookup domain name from a certificate fingerprint. I'm not aware of such registry.
The certificate used by an FTP server does not need to be the same as the one used for an HTTP server (which is shown by the https://www.digicert.com/help/).
Yes, each subdomain can have a different certificate.
If you show us, what fingerprint you get and the hostname, you may get a more concrete answer.
You can also try to use an FTP client that can verify the fingerprint against trusted Windows root certificates. So that you do not have to try verify it manually.
For example WinSCP FTP client does that (FileZilla does not).
(I'm the author of WinSCP)