I felt the same way -- excitement gave way to annoyance that this bug could render all my work useless. Most annoying is that Adobe have known about this for some time.
You're right, the problem is that Flash doesn't send cookie data with the upload (unless you're using IE (or happen to be logged in with IE)). A workaround I've seen mentioned for other platforms is to pass the "session id" via a URL query parameter. Domino can't use it that way though.
I've not given up on it yet but I need to step away from it, as I've already spent way too much time on it and resolving bugs like this can takes hours and days to solve.
Although, if you want to pay me to find a solution, that's another matter....