Also happened to some guy on OTP.
That Deus Ex Extractor and Decompiler is a fucking menace. Just now I wanted to extract some textures and I chose the target folder as the root of my Deus Ex installation, without realising that it erases the folder you extract into first. Not only would I have lost the replaceable Deus Ex files themselves, but all my textures, meshes, sounds and classes i.e. several weeks of work (and if I hadn't only started modding DX recently, potentially months' or years' worth). I would have put my fist through the monitor if 'twere not for the judicious use of a file recovery application, which seems to have brought the most important stuff back from the brink.
Whilst this has impressed upon me the importance of backing up; what is the point of it, and why doesn't it warn you first?!
The program does work but not intuitively. When providing a destination for extraction, make sure it is an empty directory. I pass this warning on in hopes this doesn't happen again.