I'm a little consufed here. "already in our DNS system" is not the same error as bad_httpd_conf. What problems are you encountering where?
As far as adding your sub-domain back in, I wouldn't think it shoudl take longer than 12 hours at the most. if it sitll won't let you add the sub-domain by that point, you should contact support.
If you've got a bad_httpd_conf error somewhere, follow the above instructions, or seach the forum for more a detailed solution.