it happens to me every so often. same thing will happen with my DLC armor in that they will just disappear completely, and will only re-appear once i restart the game back up.
Are you using cloud saves for Halo 4? I had the same thing happening to me. I was initially using cloud saves then moved all my game save data to the hard drive instead and everything has been fine since. Hope that this works for you.
my LE spec unlocks will show up then be gone then show up then be gone