I had something similar happen to me when editing a feature dataset. I finally figured out that if you import a feature class into the feature dataset while you are editing and do NOT save your edits, all the data in the imported feature dataset gets blown away. If you save your edits, then this does not happen. If no edits are made and you exit the editing session (thus do not get prompted to save your edits) the imported feature class attribute data goes bye-bye.
I was in and out of editing sessions so often that I did not pay attention to whether I was in an editing session when I imported a new feature class into the dataset. I was messing around with topolgy rules, adding data as I went along. Mainly my error, but ESRI programing rules should not allow you to be able to add features to a dataset during an edit session when this type of thing can happen. Thank goodness I work on copies and not the original data.
Not sure this fits your situation but I came across this when searching for why my data was getting blown away and finally did my own troubleshooting based upon a momentary epiphany. If not you, then perhaps someone else will benefit from my post.
