Altering a hard linked file in one location seems to destroy it in another location
A friend of mine found the answer for me. Apparently OS X has a function writeToFile:atomically, which causes a copy of the edited file to be made, then, on saving, replacing the original file with the copy. Since the copy exists in a different place in the hard disk, it has a different inode number. So after the save, the opened file points to a new location and the data at the original inode is removed. This causes the other copy of the file to now point to nothing at the original inode location.