Video missing

OK here's a new one. Dropped an Mp4 into the timeline, all good. Added a cropped background element in the foreground as a title bar, added two layers of text. Easy. Plays back fine. It's about 27 minutes long. Estimated output time 74 minutes, which is ok since I'm just going home so it can work overnight.

This morning the output is complete, but the resulting video is just white with audio. Worse than that, the video in my storyline is black. All the actual video is missing. Opacity is 100%, not cropped or transformed, normal blend mode, everything normal. Just missing.

After a restart, the exported video would play inside MPEG Streamclip (oh how I love thee, MPEG Streamclip) but it was universally about three seconds out of sync. Video in the affected storyline is still blank, although the original in the event browser is fine.