Should not make a difference. But remember I said that this "reduces variables", leaving me to think about my webservers differences. Being case sensitive would be one of those. Windows is looser than linux when it comes to folder names.
I have used Filezilla and WinSCP just as you described.
As Raymond said in the other post (we are cross posting), get rid of everything certificate. I I would add, check to make sure it is gone (for educational purposes). So as he said, first use the site admin menu >modules>activities etc and use that to delete the certificate activity. Then follow Raymond's step by step to see if it worked, making his indicated corrections if it did not. That would be using Filezilla to see if the mod/certificate module existed and phpMyAdmin to look in the database called moodle for tables that have certificate in their name (perhaps mdl_certificate). Keep following his instructions and you should come out the other side.
Warning messages are scary, so I offer this. When I first started Moodling, I placed a large smoky quartz crystal on top of my PC before I used phpMyAdmin or looked at a php file. Today, I have given up those kinds of materials aids, to a more spirtual approach. It is all about the mind, so I take a slow deep breath and quietly drone the Moodle Mantra, repeating this as necessary.