Remove subdomain

I have tried to remove a subdomain I created. It should be a simple process but the directory folder still shows up. I'm a beginner so please bare with me. Here goes: I added a subdomain, which I have done 3 times before without a problem. What I realised I did wrong this time was I didn't add the /public_html/ in front of the subdomain so the folder was created in a different location then my 3 other websites. So I decided to remove the subdomain and make a new one with /public_html/ in front. It went fine with the removal. It was gone from the "addon domain list" but after I created the new subdomain, went to file manger I saw the old folder still existed in the directory. I thought it wouldn't make any difference but I can't seem to get my newly created subdomain to work. Now I might be doing something wrong, but I have created 3 other wordpress websites and now I can get this one to work. Can it be that the first subdomain I created without /public_html/ and the removed again is interfering with the new one? And how do a remove the old subdomain folder from the file directory? Thanks in advance.