Krish - While it's not really spelled out anywhere specifically, it's always best to not be doing other things on your computer while a free-space wipe is running.
The reason is because the less you have running during an Eraser run, the more total files will be not in use, thus allowing Eraser to get into the freespace in more files to erase it.
As far as risk goes, it's problematic at best. I seriously doubt you'd hurt anything, but why take the chance? All I'd expect to see - at most - would possibly be a slow-down of your computer while Eraser was running if you were trying to other things at the same time - or Eraser taking a longer amount of time to finish its' run.
Just run your free-space wipes at night when you're not on the computer (or start it off right before you leave for work), it's more effective and probably faster that way. Pete