It can also be indicative of an eye infection... Sunken eyes are a symptom general poor health so it's hard to find out what it is without going to a vet, it could be anything from simple dehydration to worms to mites to something quite serious. Best bet is to just keep her happy as you can and get her to a vet as soon as possible.
I the mean time, make sure she drinks plenty - the fact that the eyes sunk independently of eachother over such a length of time sort of leans away from the dehydration idea, but it can't hurt to keep her hydrated. Make sure her water is freshened up frequently - snakes are naturally wary of still water sources - next time you mist her enclosure make sure you make some sizable droplets on the wall near her, my snake prefers to suck these off the wall when she's feeling vulnerable around shedding as opposed to drinking out of her dish. I read in one of mike swan's books that this is because they are more sure of the droplets being fresh and parasite free.
Good luck with it man, i hope it all turns out ok - just go to the vet and they'll sort it out - try not to freak out in the mean time - though i know it's good to share the worry a bit