Cheers guys.....
From what I have read and the research I have done it seems like the only risk is that a file may corrupt as the defragger is saving the file. And you play the same risk whenever you hit the save button in solidworks....fun huh?
Other things I've noticed:
Unfrag and Ecosqueeze...
The official line Solidworks is taking on Unfrag.exe is that it doesn't support Unfrag and that any problems that arise from it's use are your own risk.
Has anyone actually had any problems with Unfrag. So far I haven't heard one bad storey. Is there a reason for Solidworks putting in that...