First, I want to say how sorry I feel for her parents. To lose a child to a lifelong illness, to watch them struggle everyday and know they were going to die, and then to have someone destroy their peace of mind knowing that she would finally be able to rest... Whoever did this - you should be so ashamed of yourself. Whatever your selfish reasons for doing something like this may be, they don't outweigh the pain you've caused her family.
I don't know what kind of security cameras the funeral chapel may have had, what kind of neighborhood it was in or what size it was, but I would think it would not be that unbelievably difficult to steal a body. With the right timing and vehicle it could be done - they didn't steal the whole casket after all. There are numerous storage facilities that have electricity, 24/7 access and climate control as someone mentioned earlier in this thread. I would check bank records of any good suspects for rent on a storage facility. Maybe check the electricity usage at the home to see if it's consistently higher than a norm or spiked after the funeral. That person would want to keep her close. A person that buried her would think that they were doing the right thing for her, that only they truly "understood" what she wanted. They would still put her somewhere safe - maybe where they could check on her.
If the funeral home just straight up made a mistake, then it is unforgivable that they have let the family grieve this long without admitting it. An honest mistake admitted right away may have made the family angry, but that is so much better than this not knowing. With the amount of construction continuously going on around San Antonio and all the growth, it seems that if she were buried, something would have turned up by now, nearly two years later. If she was still in the area.