Nevermind, I know what your problem is. Nothing was deleted, you simply can't see it.
Go to dependencies, and move the second dependency up. This may sound confusing.. but it will work.
Everytime it happens, move the second dependency up. No matter what dependency it actually is, it's always the second one, and it always goes up.
Don't ask how I figured this one out.. I really don't remember.
Edit: It forces the editor to reload dependencies, which it does not do on start-up. If you have a map with dependencies, you cannot view, edit, etc any unit / doodad / anything else connected to the dependency until you order the editor to reload it's files.
Hopefully.. Blizzard will patch this in the future.. and have the editor load whatever dependencies the map is currently using.
It's extremely painful.. I have to operate my map in 2 different modes: Dependencies on, and Dependencies off. If they are on, I can view / move / edit
placed units using the dependency. However I can not edit them in the data editor. If they are off, I can edit my custom abilities, and any unit not requiring a dependency in the data editor.
I'm not sure if that makes any sense.. but basically the GE fails epicly hard right now.