Have you actually lost the data (as in wiped) or is it that you cant find it? I deleted a sub folder in one of my libraries and lost the entire library set of files, so I created a new folder in the library and named it the same as the one that had disappeared and it said that the folder already existed and did I want to merge them? I said yes and magically the old files reappeared.
What happens when you do a search in explorer for one of these missing docs?