Do you believe that WinsCP did something wrong? Do you have any logs to show that?

Otherwise, you better seek a support with mailwizz community.

WinSCP Version: version 5.17.10(build 11087)
Windows 10 Home 2004 Version
Transfer Protocol: SFTP-3
Crypto protocol: SSH-2

Hi, I'm experiencing a weird problem while upgrading different versions of mailwizz to my server.
Basically it copies all the directories but there are extra copies of directories in two specific folders, /var/www/html/customer & the front end dir. Basically while uploading from my desktop to my server I clicked Overwrite & Yes to all; which I believe is the right way to upgrade existing files/folders. Anyways my mailwizz app basically crashed because of this. I'm not sure if you need error messages BACKEND URL page basically reads:

404 Not Found
The requested URL was not found on this server.Apache/2.4.29 (Ubuntu) Server)
Front end URL error internal server error.

I basically followed this youtube video for upgrading
https://www.youtube.com/watch?v=018HcIW0BG4

Please let me know if i need to add more info, I basically don't know why the upgrade didn't work, is it because of the extra copies of the files/folders? did it not properly upgrade or overwrite files with same name?