Triggers and other Game Objects lose data after updating Unity

We have a game that's been in development and out in the wild since Unity 2.6. The game needs another key update, and we want to go to Unity 3.5 to do it.

During the update process, I grabbed a fresh copy of the game, and installed 3.5beta. Upon building the game and looking at various bugs to resolve, we found that many triggers and other game objects that had outputs set by Level Designers, were missing all of that data. In other words, the database of game objects is still there, but whatever connected the dots is gone.

Has anyone had an experience like this before? We also experienced something slightly like this before, and it seems to keep cropping up.

Example:

1. Start the game

2. Game story Begins

3. Tutorial Begins

4. Player leaves Trigger that's set up to kick off the next part of the tutorial

5. Nothing happens

6. View scene in Unity - the trigger's outputs are empty.

Found this in many triggers and some prefab game objects, across the entire game.

Thanks.