Share your experience!
I don't think I have encountered something similar before. Do you use the default phone and contacts app? Can you check if the same occurs in safe mode?
Do you have sync enabled? I guess somehow you could delete a contact from google or other accounts and have it reflected on your phonebook.
Really strange, any filters applied then? You can check under contacts.
Are you willing to give it a try in safe mode for a couple of days?