This has happened to me a couple of times. I have lost contacts that were definitely added in the default Android contacts app.
I suspect it is whatsapp, because it only seems to affect contacts added through it:
In whatsapp, i have selected add to contacts, and saved the contact in the built in Android contacts, and a while later, this contacts have disappeared (been deleted) and in whatsapp the chat names have reverted to telephone numbers, and i have to add them again.
Has anybody experiences this?
I am not sure if it because i added then from whatsapp (i.e. if other contacts have been deleted), but that's the only place where ive been able to verify it, and the disappearing contacts seem to only be people I have added to my contacts from within Whatsapp.
I guess it would be a WhatsApp bug, but still