> Is there a way to fix this well after the fact?

Yeah, you can get in there and do some work at the individual surface level to repair this. It is a bit involved but here is some explanation.

Check out this post which explains how to do a basic "untrim" which can be used to erase a hole on an object and recover the underlying surface: http://moi3d.com/forum/index.php?webtag=MOI&msg=444.4


What you need to do is first select the surfaces (faces) that make up the protrusion of the view-port from the main body. You do this by doing a second click on the object. Your initial click on an object selects it with "whole object" selection, then after that an additional click will drill-in to a sub-object of either an edge or a face. Edges get precedence so to select a face/surface you need to zoom in a bit until you can grab a spot that is in the middle of it somewhere not close to an edge.

You want to select all the surfaces of the protrusion, and then do an Edit/Separate - this will detach that protrusion from the main body and make it into an independent separate type of assembly. (note - if you do an Edit/separate with the entire object selected it will break into all separate surfaces, but if you have a set of faces selected it will separate that connected set as a sub-assembly, then you can do another separate to break this into individual surfaces if you want).

Now hide that sub-assembly, then you want to go in and erase the hole for where it was - reference the above post for this procedure. You may need to erase some trims on the sub-assembly as well to restore it. Once both of these parts are all restored, center the view-port sub-assembly and reapply it to the main body, by boolean or trimming.

If you want to post the model I can show you some screenshots of this procedure on your actual model.

- Michael