For (near)-perfect scans I can't think of a way with most manuals. With manuals that are ringbound (like the old Deluxe Paint II manual) I supposey you could carefully take all the pages out and then put them back in again.
For other manuals you are going to end up having to fold them flat which will screw up the bindings no doubt.
But maybe you should consider the worthwhile cause your sacrificed ebay purchase could be helping
Just had a thought......handheld scanner......