Select shots of the ship which couldn't be found have been replaced with CGI.
There is one shot of the Enterprise in "Encounter at Farpoint" where we see the Enterprise delivers an energy beam onto Farpoint station that reveals the squidy space creature. That shot of the Enterprise is not only new, but the beam itself now emits from the actual phaser array instead of the Captain's Yacht (Center of the saucer section). So it's both a redo and a fix.
What makes this change a bit sad is that after using the same CGI shot of the Enterprise for "Code of Honor", the restoration team actually found the footage for the model shots of the Enterprise from that angle, so every episode after "Code of Honor" now features the real model shot instead of the CGI shot.