Because temp files delete over time. I don't know about this second theory but they might delete if you play a certain amount of additional sessions. Additional sessions as in quitting the game and booting it back up. Making sure to save your temp files (and upload the files to your file share).
I really think the MCC should bring back in-game storage for screenshots and film clips. The Xbox thing is nice but not everyone may want to use it, especially when 3 (4?) out of the 6 games on the MCC have this in their original versions. Wait, does ODST allow film clips in Firefight? I'll have to check.
Sadly, only Halo Reach supported taking film clips in Campaign, Halo 3 and ODST only supports screenshots from there. If the MCC still stored screenshots and clips then they could have upgraded Halo 3 and ODST to enable taking campaign clips.
I was kind of hoping they might do that for the original versions, but they are never going to do that now, so the MCC is— was my only hope, until they decided to do away with the in-game storage.