Overwrite file issues

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?

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.