Except that they're not. Once the sync was completed, I rebooted the system, started in maintenance mode, ran a filesystem check/repair on Disk 4 (which failed again like last time this happened), restarted the array normally, and all the files are back now. I don't explain it because I'd agree that sync has nothing to do with missing folder contents (even though the folder itself is there). All I know is that this is twice now that this process has worked so I don't know what's going on. Everything seems to be working properly now. Go figure.
Here's a diagnostic. Maybe you can figure it out.
storage-diagnostics-20240212-1158.zip