Deleted second subdomain but how do I delete related files

[ereader]

… using file manager I get permission denied error message.

[Admin]

You should just be able to delete the folder of your old subdomain. Or at least navigate to the htdocs folder of that subdomain and delete the contents.

That is, of course, assuming you haven’t messed up the permissions of the files and locked yourself out. In which case, you can’t delete the files anymore, with or without subdomain.