I havent tried to move anything yet.
My problem is that it is taking forever to scan for recolours everytime I click the move/delete button. I think it scans the entire download folder, and not just the folder being used. I may have to resort to moving everything out of downloads except the folder I'm working in to make this program work at a reasonable speed.
Also, it looks like the site was just updated with a new version after a bug fix, that might fix your problem.
*edit*
Broken down into smaller batches, this makes for pretty easy deleting. I still havent tried moving things with it, though. I think for just sorting items into categories, Clean Installer would do the job faster since it doesnt have to scan for recolours. Still, as far as content management goes, this is a pretty good tool. I like being able to identify each item by a thumbnail rather than trying to figure out what it is based on a texture grab.
Now if only someone would make a tool to clean out orphaned meshes and textures