1. What happens to the alternate level 2 colony tile I had been using?
I can't provide any definitive answer, but based on my experience with the base game, I would assume that you relinquish all claim to the second level of your colony once you downgrade. This interpretation would mean the alternate colony tile would be returned to the supply immediately.
2. What happens to the worker that was on the alternate level 2 colony tile?
Again, no definitive answer here, but I would think that the worker would be immediately returned to your supply upon downgrading, to be available for use the following year.
3. Do I forfeit the ability to not discard resources in the end of turn phase?
You will remember that the Atelier phase comes just prior to the "Discard Cubes" phase. My interpretation, for what it's worth, would mean that since you have downgraded your colony prior to the Discard phase you would have indeed lost the ability to keep all 12 cubes.
My interpretations aside, the rules for the mini-expansion read as follows - "When advancing a new colony level, a player can take one of the 4 alternative colony tiles (of the level he would have reached normally) and place it on his personal board, above the default level. He has now the new powers described below until the end of the game (instead of normal ones)." "Level II (grey): for a worker action, this player doesn’t discard any cube this turn during phase 6".
These two clauses would seem to indicate that despite downgrading prior to the Discard phase you would not be required to discard any cubes; furthermore, it sounds as if once you have upgraded to an alternate tile, you would get to keep it and the special abilities it allows even after downgrading. It seems hard to believe that this was the designer's intent, but that's how I would translate the rules as written. This is an intriguing set of questions and one I hope the designer weighs in on.
Edited to include rulebook references.