Once I put my SS into DS, Emerald deleted (again - now with all non-event legendaries and most useful TMs)...Any idea why?
You answered your own question.
Your DS seems to be a bit weird...it always works for me.
Do not have a GBA game in your DS when you are going to play your DS games.
You can still play Emerald, just don't have a DS game inserted when you play. But, that means you will not be able to migrate anymore.