If I understand, you are asking if the following situation would work:
1. Book a ticket with you SM number
2. Wait until the 5-day window and get the upgrade
3. After getting the upgrade, switch you SM number for an AF number (or some other SkyTeam partner).
I am not sure what would happen to the upgrade. Definitely a hazy area that DL does not define. If you try it out let us know the results.
You would definitely earn miles on AF in this scenario though, so your attempt to rollover 49K would still be entact....I believe.