Sounds very odd to me as well–haven’t encountered before. If the clips otherwise seem to be there, but just an empty black box in the timeline, try deleting all of the renders as well. Maybe even Optimized and Proxy media. Also, see if toggling from Better Quality to Better Performance to Proxy to Better Quality, etc. does the trick to sort of kick things in the pants and refresh the views.
Deleting Preferences is a solid troubleshooting technique, as is rebooting the machine (do it cold, not hot–meaning total shutdown let it sit for a minute or two; I know, sounds like archaic, old-school, irrelevant instructions, but it brings me piece of mind that a hot reboot doesn’t when the system seems to burp somewhere–can’t hurt :-).
If behavior remains, try duplicating the Project or pulling something forward from one of the Backups pre-problem. Maybe there’s an effect hanging things up.
Anyway, a few extra knobs and switches to fiddle with. Definitely disconcerting to have empty boxes that otherwise work.
— Joby.