Deadly DNS Entry

I recently setup a few new webservers, had everything working fine, I am giving each website a dedicated IP, I was trying to tweak the DNS output on dnsstuff.com, I was getting a warning for:

"Mail server host name in greeting"

So, I added a "a entry" under the particular domains DNS to point to the main server IP, that did take care of the "mail server host name" but come to find out that really screwed up alot of stuff..

For instance, the site that has the dedicated IP and the new "a entry" will not work now unless I change the sites IP in the WHM to point to the main host IP, If I change it back to the dedicated IP or any other dedicated IP, it just gives a list of "dir files" for that domain.

Is there anyway to get rid of this "a entry" that I have added for that domain to take it back to normal.

Also, if I take a domain name that is already in the system and working fine with its own dedicated IP, and try and move it to a new dedicated IP it messes that domain name up also, and then can only be accessible by changing it back to the main server IP..