Sorry, you will have to give us a way more information. Screenshots, log files, etc.
Did you test the same with another SFTP/SSH client?
I do not think this has anything to do with hostkeys.
I have two virtual servers in the datacenter that I have used. I install Winscp on my windows client machine. I installed openssh on my Windows 2012 servers. I connect to one of the servers as ssh with winscp. I can make my copy process. Then I want to connect to my second virtual server with open ssh installed in the same place, same winscp client. But it does not connect to the second virtual server. Although I enter the second virtual server information, it connects to the first server I entered first every time.
What is the connection method to two windows servers via winscp client running on a windows. I could not find information on this subject.
It's probably a matter of host keys. When I look in the registry, there is only one key "[HKEY_CURRENT_USER \ SOFTWARE \ Martin Prikryl \ WinSCP 2 \ SshHostKeys]".