Does this?
Your point is obvious, but not specific to persistent environment. Things are getting broken sometimes.
Actually, back in 2009 when first message about Phantom appeared, I've got a message from team in Stanford. THey did an experiment about things we discuss.
Relatively big Java program was stopped in the middle of work, serialized to (I believe) XML and some objects were removed from that XML. After that program state was de-serialized and program continued to run.
Experiments shown that modern code degrades quite gracefully in such cases. Most of time problems were not global and affected just parts of program's abilities.
But again, it is not a persistent world specific problem.
If your code is wrong, no matter where index lies - in persistent memory object or in file. Index will be wrong.
The question is how system must be built, what kinds of services it must provide to limit app ability to shoot itself in a foot. That is one of the goals of this project.