I received the secondary application on July 8, after which I promptly contacted MD admissions and asked them to verify if I should send my supplemental after I submit my KH application. They verified that I should. Did you get the email about the supplemental not having been received this morning? It was unsettling. It said, "According to our records, you have not yet submitted your Supplemental Application to Stanford Medicine. If you intend to submit the application, we request that you do so on or before the final deadline of October 20, 2017.
If you intend to withdraw your application, please complete this process online as soon as possible."
I'm not gonna sweat it, though. They know that I've contacted them about the KH scholarship. The fact is that, according to what I read somewhere, apparently they review your application is sent to the front of the queue if you have a KH scholarship PIN. So, for those applying for KH, rest easy, you won't be penalized for your semi-late application.