I know alot of these posts are kind of old. But the only application I submitted through SOPHAS was a pain in the ass regarding my reference letters. One of my references told me he couldn't locate the notification from them, it was probably just buried in his inbox. It was no big deal to me I figured I would just enter my application and click an option to re-send it (the way all my other applications do), but there wasn't an option for that so I removed him and added him again (the only logical thing I could think of). A week later he had only gotten the notification saying he had been removed, I call SOPHAS and lo and behold the only way you can re-send the notification is by calling their customer support line (doesn't say it anywhere on their instructions/application). And of course they were snotty about it.