It's indeed a similar situation, but you are actually the first one have this problem. So a support for multiple TLS/SSL certificates was never implemented (contrary to multiple SSH host keys).
No, I don't have any old log files from our previous release. Since we never had any issues I don't think I ever even knowingly logged anything. So, because we're using FTP, not SFTP, what is getting updated in the WinSCP.ini file is the certificate not the fingerprint? And there's no way to check multiple certificates? My assumption is that it's a similar situation where there are four target servers behind a load balancer and depending on the moment you could get any one of them. I've seen one of the 4 below at different times. I'll check with the vendor to see if that's changed recently.
upload.perfectcompliance.com:990:tls=a9:c2:55:20:d3:49:74:e3:3a:2c:84:16:fa:ad:63:a1:2a:cd:08:a4
upload.perfectcompliance.com:990:tls=12:ad:a0:f5:40:fa:f1:e5:67:f9:7a:35:ea:17:44:27:c4:6d:2b:97
upload.perfectcompliance.com:990:tls=a3:5a:07:27:c6:43:72:4a:e4:28:69:af:83:18:af:22:eb:fa:34:17
upload.perfectcompliance.com:990:tls=a6:ae:f0:eb:b4:fa:56:f3:78:df:6d:22:2f:25:56:aa:59:0d:1a:f6
Note that the message says "server's certificate", not "host key". "host keys" are for SFTP/SSH, not FTP.
WinSCP does not support multiple certificates for a single hostname.
I cannot imagine how it could have worked in 5.5.2. Do you have a log file from that version?
I'm using WinSCP 5.11.03 to FTP a file to a vendor site using the FTP file protocol. We just upgraded from 5.5.2 (Build 4130). I am using the same WinSCP.ini file I have been using for years. I get "The server’s host key does not match the one WinSCP has in cache". After a few times it will eventually work when it hits the target host whose fingerprint is in the WinSCP.ini file. I read the solution about multiple fingerprints in the WinSCP.ini and attempted to try that using the command line as outlined in the solution but I don't get an option to "Add", only "Yes", "No", "Cancel". "Copy Key" options are available. I tried adding the fingerprint manually to the WinSCP.ini file using a semi-colon between fingerprints as suggested but it doesn't seem to work.