I have added this issue to the tracker:
Issue 2247 – Limiting SFTP version to 3 with non-well-known SFTP servers as a workaround for interoperability issues

I'm sending you an email with a development version of WinSCP to the address you have used to register on this forum.

I see... moving foward, I'll make sure all my SFTP connections are set to version 3. Thanks again for the help.

Your server was likely updated. Either it newly added (broken) support for SFTP 5 or its existing SFTP 5 was broken. FileZilla supports only SFTP 3, so it does not see the problem.

Few clients support SFTP 5. So it is unfortunately common that non-mainstream SFTP servers, that do support it, support it badly. Because it is poorly tested.
I'll consider defaulting WinSCP to SFTP 3, unless connected to a well known SFTP 5 server.

Changing it to SFTP protocol version to 3 fixed the problem. Thank you for this tip... but I now have a follow-on question. I use a script to automatically connect to this SFTP site on a daily basis. I've used the default connection settings for over a year without issue. Why the issue all of a sudden? What's the difference between protocol 3 and 5?

Try limiting SFTP protocol version to 3:
https://winscp.net/eng/docs/ui_login_sftp

The connection is being made to the same site. Attached is the log from FileZilla.

WinSCP is showing all the files that the server has provided. Are you sure you are connecting to the same server using the same account?
Please post verbose logs both from WinSCP and FileZilla from the same moment.

I am using WinSCP to sync files from an SFTP site to a local drive. Lately, WinSCP is no longer seeing new files being uploaded to the SFTP site. If I use FileZilla, I can see the new files. I've tried with "Show Hidden Files" both on and off, but still does not work. What type of issues can cause WinSCP to not see new files? Attached is a picture comparing the two tools, WinSCP on the left and FileZilla on the right. The red box is the differences in files. I've also attached a log file of the WinSCP connection.

Thanks,
David