Very strange! I wonder if it might have also worked to use the File ▸ Save and Rebuild Search Index menu command. That would force the program to go through and read all of the .txt and .rtf files again, which is a slower process than just reading the index file as it does on load. If the index file was damaged, it could explain why everything came up empty looking.
It might not be a bad idea to run that command no matter, just to be on the safe side.