Did you try increasing connection timeout?
https://winscp.net/eng/docs/ui_login_connection
If that does not help, please post session log file.

Hi,
I have a client that is navigating to a folder that contains 128,000+ files and getting timed out. We can see the file count incrementing and she can access directories with fewer files with no issue. We changed the Remember last used directory setting to keep her from landing in the large directory immediately on login, but they would like to be able to access it even if it takes awhile.

We tried increasing the server response timeout but that did not help.
Is there a timeout setting that would specifically pertain to the transfer that happens when retrieving the directory information from the SFTP server?

I saw SessionOptions.Timeout mentioned for a similar issues with scripts, but I am looking for a GUI setting.

Thanks,
Jon