My college website www.chenabgrw.edu.pk was published on weebly. I purchased a new hosting service and updated nameservers. I installed wordpress on a subdomain www.new.chenabgrw.edu.pk After designing new site I deleted my weebly site to shift subdomain new.chenabgrw.edu.pk but I am still getting a 404 error of weebly. For now I have made an html page on weebly having javascript of on page load redirect function which redirect main domain chenabgrw.edu.pk to new.chenabgrw.edu.pk
This isn't going to be (would not have been) a Weebly issue, but instead a DNS issue. Or you were seeing cached information from your browser/network.
As it stands now, you have a CNAME for www.chenabgrw.edu.pk pointed to chenabgrw.edu.pk but chenabgrw.edu.pk is pointed to a Weebly IP Address (199.34.288.67). In other words both the Root and the WWW are pointed to the Weebly IP Address.
So, seeing that your NAMESERVERS are pointed to hosterpk.com you would want to log into the hosterpk.com account, where you manage your domains DNS, and point the Root Domain chenabgrw.edu.pk's A Record to 69.162.90.106 ~Then you should be able to set the domain to use chenabgrw.edu.pk instead of new.chenabgrw.edu.pk
Keep in mind that after you make DNS changes it may take time for them to update. You can use a service like http://www.who.is/dns/new.chenabgrw.edu.pk or http://www.dns-checker.com/dns/new.chenabgrw.edu.pk to see if they have been updated. THEN your browser cache or Network might be showing you out-dated info. Clearing your browser cache and or restarting your network can help.
If you have any issues updating your domains DNS, you'll want to reach out to the provider where you manage your domain's DNS.