IP Migrations Wizard - 2 issues observed

I'm in the process of migrating website IPs (both shared and dedicated) to a new subnet on the same server. I've run into 2 issues so far. First issue, and most critical. I found migrating customers that manage their own DNS externally (ie, godaddy, network solutions,etc) breaks their website. cPanel display the default webpage of: "SORRY! If you are the owner of this website, please contact your hosting provider: ------------ It is possible you have reached this page because:...." When I looked at the httpd.conf files the old/new IPs look like they are properly configured. Shouldn't the site respond on both old/new IP regardless of who holds the DNS? This broke about 30 websites and had me scrambling to contact customers on a less than desirable time frame. Second issue, which was easily fixed. One customer's 3rd party SSL certificate was uninstalled! When they notified me, I went to their control panel and sure enough the "install" button was clickable. It was an easy fix, but why did the SSL cert get uninstalled? I have another server to renumber and would like to get an idea of what's happening here before I move forward with the other server/subnet. I tried opening a ticket when this issue was noticed, but it was a 16 hour wait so ended up taking care of it by completing the migration and calling customers. Any help/ideas would be appreciated. Thank you.