Can you answer the questions you missed out on the form please. With just your domain and a "404" it's difficult to give you any useful advice.
What client are you running ?
what command did you run ?
Can you provide the full log please ( with the debug option if the client you're using supports it).
You've edited and added the data - thanks - I will take a look
With certonly ( see the manual ) you need to be giving a little more information - such as webroot ( for where the root files for the domain are) and what domains you want
would obtain a single certificate for all of those names, using the /var/www/example webroot directory for the first two, and /var/www/other for the second two.
I have tried to find acme-challenge on the drive with find tool, but I have somehow fucked up months ago. So the question is, is there any way how to restore the “acme-challenge” directory and data within the folder? (Run command/delete something).
if you create the “.well-known/acme-challenge” folder in your webroot, and then add a file called “test” at webroot/.well-known/acme-challenge/test and just the plain text contents “success”