I've had two 4S iPhones for over a year now (first one fell and broke and I replaced it with a brand new one).
With each of these phones, about every month or so, it goes through a period where it will delete contacts entirely out of my phone book. Sometimes it'll compulsively delete only the most recently added 4-5 contacts, other times it just chooses randomly. If I don't have text messages from these people saved in my inbox, I lose their numbers entirely.
The OS doesn't seem to affect this issue - it's been consistent through 3 different software updates at this point.
No idea what to do! I have all my info backed up to iCloud, which backs up daily, but that also doesn't seem to make a difference in saving my contacts.