I'm currently experiencing the same problems as described above. I don't exactly know why it happened, but I'll try to describe it. Yesterday I accidentally exported my application XML fully locked. After that I did something stupid so I had to reset my application using the XML. I then noticed I accidentally locked it, and edited the XML tags "isManaged" and "pubManaged" to unlock it again. I then updated my application using the XML.
24 Hours later (now) I noticed some unused related fields had suddenly gone "Related Field(UNKNOWN)" so I deleted those. I also noticed that the "Related Field(Contactperson)" had suddenly disappeared and I was unable to select it. About 15 minutes later after updating the field I'm able to select it again.
I don't think it's bug worth creating a defect for, but i'd like to report it.