Sorry for my lack of clarity in the previous post: As soon as you confirm your upgrade the miles will be deducted soon after. However, you can put the upgrade on hold, I did so this past summer. It might have been an anamoly but I don't think so:

I called EK and made a booking. The upgrade was on hold until the paperwork was completed (which was over a period of about 7 days I left it till the night before) and then the miles were deducted. However, the agent had no problem just creating an upgrade and not deducting any miles.

Cheers,