Mission data lost on Legendary completion

Thought I just beat the game on Solo Legendary, but did not get the Legendary ending. Turns out all my level completions for the first three levels was reset. WTH? Anybody else having this issue?

The only thing I can think of is that I turned on IWHBYD/GBP skulls after the Requiem mission and maybe the previous data was lost. Why would that happen?