I don't think that there's anything that you can do in DOSBox. Operations are pretty final and there are no safety nets. You're probably limited to what you can achieve in your host OS. If it's Windows, the first thing to try is Previous Versions. Right-click on your Games folder, then choose Properties, go to the Previous Versions tab and, if there's a previous version of the games folder listed, select it and choose Restore. As a last resort, there are always disk recovery tools.
BTW, I had to test this because I almost didn't believe that simply doing "copy *.*" would wipe out every file in the directory... and it's true... and it's still unbelievable. Surely this behavior wasn't in MS-DOS. I'm really surprised that this has been overlooked or not addressed in DOSBox after all of this time. Wow, it's even in the latest SVN builds. It seems like Error Handling 101: if the user neglects to include an important parameter, kindly abort and inform him, don't wipe out every file in the directory.