404 error after a successful publish

I'm Scratching my head here because after doing an update to a web app that sits in the sub structure of one of our internal sites, I'm getting a 404 errot. Despite verifying and making sure that I was following the same process I had used prior to this publish.

This illustrates the above:

Now, to make sure I've provided as much insight into things that are unique in this publish vs others that were successful and rendered the expected results consistently till now:
1.This server (a dev/test box) was moved to a new domain week before last along with it's production counterpart and the database server that each web server talks to for the web applications hosted on them.
2.For expediency this server was cloned to the production site as we had a clean, current, and successfully tested deployed version of the core site on the dev/test box.
3.While it wasn't a change, I am unsure if it would have a certificate that was on the box would have an impact on the ability to successfully publish future updates on the same server in the new domain.
4.In addition to item #3 I'm further baffled that if this is being caused why is that that existing apps on both the production server and this dev/test box continue to function as they would be expected to. It was only the act of publishing the update that resulted in this behavior. So this would seem to suggest to me that the issue has something to do with changes made during the publish (which has not been altered from prior publishes).

Any thoughts on this that can aid me in getting this resolved greatly appreciate.

Ken...