@ChipAddict
I have run into the same problem. Currently there is no way to queue messages for your core from the cloud. You will have to implement some other method to have your core check for pending messages - possibly a google drive, or your own site - and then pass it a custom ‘stay online for firmware update’ message. This will tell your core to not go to sleep. Then on your other site you can take the notification of the core being online, check that the core is in fact online with the spark cloud and then pass along your firmware update message via the cloud.
I think the Spark team is working on improving this capability for the future - as I am sure the electron will need this behavior. They are currently working very hard on getting ready for the photon. I expect we will see in implementation probably after the photon and before the electron 