First, I think you need to determine if the eyes are really sunken or if the tissues surrounding the eyes is swollen, giving the appearance of sunken eyes.
If the eyes are really sunken, it's a condition called Enopthalmia. In snakes it is caused by one of two things. Either dehydration or ocular scarring (phthisis). Since it is bilateral, you would rule out ocular scarring from mechanical means, but would consider pathenogenic scarring (possibly pseudomonas, proteus, serratia, or other pathogen). If it is caused by dehydration, then you need to find the cause of that. Dehydration can be caused by husbandry (probably not the case here), pathogens such as intestinal parasites, stomatitis, etc., administration of nephrotoxic drugs such as Aminoglycosides, overuse of certain other antibiotics and antimicrobials, anthelminths, etc., such as Metronidazole (especially in Indigo Snakes and Tri-color Lampropeltis) and Thiabendazole. Normally you would think that dehydration severe enough to cause Enopthalmia would be evident by loose skin, disecdysis, etc. and would be accompanied by anorexia, especially if the cause were pathogenic.
I think, if I were you, I'd get the snake to a veterinarian that is experienced with treating snakes and find out for sure what is causing it. While the sunken eyes, in and of itself, isn't a big issue, the underlying cause could be.