Makes sense but authentication isn't handled by a cookie, it appears to be a request header sent by the browser.
CODE
Authorization=NTLM TlRMTVNTUAADAAAAGAAYAF4AAAAYABgAdgAAAblah blah blah gBuAC0ANgAxAO9QG6ocLV80AAAAAAAAAAAAAAAAAAAAADukLJ1BYZIKL+5VW7uEpE29bEr3DjH4xg==
ok. I was way off the mark in my first response. We could widen the Uploader interface to allow javascript to specify additional headers (perhaps Authorization, and X-* headers), but I don't know that this would solve your problem.
As far as I can tell, NTLM is a challenge/response protocol and each header is different from the previous.
Perhaps there's a workaround in an application level mechanism? Something like embedding a temporal token in the served page that's associated with the session and the upload handler checks for this?
I know this is probably unsatisfying, but look forward to your reaction and will continue to ponder it with the team.
best,
lloyd