That shouldn't be a problem, BB does incremental backups continuously. So if I came back from a trip where I had to download a DNG from PS to work on for a client, I could just replace the current DNG on my system, with the one from the laptop. Then when BB came to that drive to back it up, it would see a new modified time on the DNG and replace the one on their servers with the new modified one.
Thanks for questioning all this, its really helping me run through the scenarios in my head.
Rob