The way I do it so I don't mess up scan files during clean up is to:
-save all my original scans before cleaning
-clean up scans as needed
-if I mess up and delete too much of one scan you can remove that file from your 'LIST OF WORKING SCANS' and drag/drop scans under 'WORKING DIRECTORY' to reload originally saved scan.
-after cleanup, I save all the cleaned scans with a suffix that designates them as 'cleaned' (I.E. scan_01 cleaned)
-after fusing, I save the fuse and I also re-save the cleaned scans so if I need to go back and try to re-fuse at a later date I have my last orientation of the cleaned scans.
Using this method I always have saved original scans, a separate set of 'cleaned' scans with proper orientation, and my fused scan. Yes, I have more than once erased more than i wanted during cleaning. I have also, more than once, had to go back and re-fuse if I found something out of alignment. Did I tell you how much i love the cleanup and fuse of David!
DAVID-CAM-1-C, Acer K11, Macro lenses for K11, Logitech Pro 9000, EOS 40D