When NikonUSA repairs a camera, they create an Invoice Repair Description that has cryptic information on it. I've noticed that there seems to be two different types of repairs happening on D800 models submitted with focus issues. Both are generally labeled Service Repair Rank B1.
If your camera was fixed for the left sensor problem I've been writing about, you'll see an item labeled Repair SC 201759. I believe this refers to a service procedure number on the problem, though I've not been able to get my hands on that document (turns out that this is a long established procedure, but it's not clear why so many D800 cameras require that specific procedure). Cameras that are repaired this way also get an ADJ AUTO FOCUS OPERATION notation, which indicates that the camera went onto the normal rig for verification of focus operation, and which sometimes causes the technician to make other minor adjustments.
Some D800 camera repairs are not showing the SC 201759 notation but additional ADJ AUTO FOCUS entries and sometimes B2 level repairs. This is probably because the camera was determined to have a mirror adjustment problem or other focus system error, not the one that is causing all the fuss.
B level repairs generally require bench testing time but not any critical disassembly of the body (which tends to be the case at C level). NikonUSA charges a fixed price on B level repairs out of warranty, which I believe is something around US$250 at the moment (and includes shipping costs back to you).
In all cases with B level repairs, the camera goes through three other procedures: Nikon checks the camera's internal data communications, they clean the image sensor, and they do a general check and clean to look for other items such as dirty mirrors, unclean contacts, or controls that are loose or jammed or not working properly. In theory, a camera coming out of a B level repair should be at or above the level of quality coming out of the factory.
This brings up something I've mentioned in passing before: many of us pros send our bodies and lenses into Nikon every couple of years (or less if we've been abusing them ;~) for something called a CLA (clean, lube, adjust). This is an extension of the tail end of the B level repair (camera put on test rigs and checked for correct operation, then thoroughly cleaned and checked). Autofocus systems do go out of adjustment after all (vibration and constant use can change mirror positions, for example, and dust and dirt can get down into the autofocus sensor area at the bottom of the mirror box).
There's one caveat with a CLA, though: if Nikon discovers something that's faulty, they will want to repair it. If the camera is out of warranty, obviously, you'll have to pay for that. Basically, NikonUSA won't do any work on a camera unless they can bring it up to the standard of cameras leaving the factory. Thus, they won't repair just one thing (scratched sensor) if another thing (impact damage that causes a crack on the casing) is present and you don't authorize full repair. This catches a number of out-of-warranty repair or CLA requesters by surprise: they submit the camera for X and find out it needs X+Y+Z and the bill is substantive to make those repairs. The plus side of this is that you'll get back a camera that is as close to new as NikonUSA can make it. The downside is that you might have a bigger repair bill than you thought.