I really don't know how else to explain it.

Do you mean companions? If so then that is a better way to explain things. As for why they disappear and how to get them back; nobody knows. Another bug to put on the list.

I think he means Faction relations.

Mavj96-
Your most likely wearing a Factions piece of clothing or armor, in that case your disguised as them and if you take off whatever your wearing, your faction relations/reputations will come back

That does make sense. I didn't even think about that possibility.

Yes I meant Faction Relations, oh well though I changed my mind on my Character and restarted anyway.