This doesn't have anything to do with the activation. If the activation is lost, for any reason, the scenery will not disappear. It will revert running in Trial mode, for 5 minutes at time. The Trial mode doesn't expire so, fact you already used once, doesn't make any difference: you can have an unlimited number of 5 minutes periods of Trial.
So, the problem didn't had anything to do with the activation.
If this happen, check you see BOTH the "Addon Manager" menu AND the "Couatl powered products" under the FSX menu bar. it's possible that buildings might disappear if FSX didn't close cleanly. In this case, a Windows reboot will surely fix it.