To wrap up the Face/Off series, a little more exploration of tissue rejection is in order so that we can appreciate the full depth of amazing, entertaining, wackiness serving as a vehicle for this movie.
All the cells in you body have a unique set of protein markers on them called major histocompatibility complex antigens (MHC antigens).
MHC antigens are sometimes called "self antigens." They let the cells of your immune system know what is you (cells with your MHC antigens on them) and what is not you. If cells are not you, they should be inactivated, destroyed, and/or eaten, because they are usually pathogens and about to do you harm, or so your immune system would reason.
There are a number of ways one's body will destroy foreign cells, here are a couple of them. Immune cells (white blood cells) travel to the site of foreign cells to eat them or cells already in the area can release chemicals to destroy them (cell mediated immunity). Or antibodies and other plasma proteins can attack the tissues via the bloodstream (humoral immunity).
What does this mean for our movie? Well, if the blood match is wrong, and/or the graft (or face) for the recipient is of the wrong tissue/blood type, that FACE is coming OFF, all right. It will not be in any shape to return to its original owner, either.
Rejection of a transplant can be dramatic, as in a hyperacute reaction which happens within hours or minutes of revascularization (return of blood flow).
(Dark purple things are stained white blood cells.)
Acute rejection will occur within a week, or months.
Chronic rejections can happen after years, even when the patient is taking anti-rejection drugs(1). With rejection, one's immune system attacks the foreign tissue. In the case of a face, that might make for a good horror movie...
(The slides of tissue rejections are all of kidneys.
I couldn't find pictures of rejected face tissues online.)
Can't you see John Travolta (as Archer) impersonating Nicholas Cage (Troy) with his face all mottled and slipping around? They could fight over the only remaining viable face, which would be Archer's, due to that blood type issue mentioned in Part 4. But I digress.
To prevent rejection, a transplantation patient must take drugs to suppress their immune system for the rest of their life (or as long as they have the transplanted tissue in their body.) These drugs suppress the whole immune system. Death due to secondary infections is very possible with transplant recipients, whether they are using "the new anti-inflammatories" or not because they are not as capable of fighting off pathogenic organisms like bacteria (whose antigenic markers show them to be foreign to one's body.) We don't see it in the film but I'm sure Archer and Troy were scrupulous hand-washers when off camera. Particularly Archer, when he was in prison with Troy's face. I imagine prison is kind of dirty and has lots of bacteria.
Prednisone is a corticosteroid immune suppressant that is commonly used by transplant patients. Dosages of prednisone are much higher immediately following surgery, and can usually be lowered over time, but rarely can the patient stop taking the drug altogether(2).
Prednisone can cause a number of side effects including; increased fat over the face (sometimes called "moon face"), shoulders, and abdomen, although the arms and legs will be unaffected by the new fat distribution; longer healing time for skin; ulcerations of the skin; osteoporosis (thinning of the bones); fatigue; and muscle weakness. In addition, people taking prednisone or other immunosuppressive drugs have a greatly increased risk of developing certain types of cancers, which a healthy immune system would help to keep in check.
In conclusion, it's a great thing for Archer that these procedures were indeed "completely reversible." He got his original tissues (including tummy fat) returned to his body and got rid of the morpho plate inside his face. If Troy's face had damage to it from rejection, it doesn't really matter because (spoiler alert 12 years after the screening of the film) Troy dies, but not from faceless cigarette smoking!
1. Merck. pp. 347-352
2. Merck. pp. 346-354