It's worth noting, just because I've seen people do this fairly commonly, that unless you have a specific reason to run the rebuilds or we advise you to, there's absolutely no need to. Especially seeing as any rebuilds that need to be done during upgrade (such as the thumbnails) were effectively already done.
We're unlikely to be able to figure out where the file has gone, now, though if you have a back up of your files I might be able to direct you towards finding that and moving it into the correct place. Actually, if you happen to still have an internal_data/xengallery/originals directory then you may still have the file.
Incidentally, we've seen files go missing in the past but generally it has happened during backup/restore operations or when moving servers and that kind of thing. It could of course have happened due to some sort of past bug or read/write failure during the upgrade but it will likely be impossible to find out exactly what.
If all else fails, we can maybe just update the database so that the media item is no longer recorded as "watermarked" but of course as the image is already watermarked it could end up giving it a double watermark which might not be desirable.
