You'd have to be crazy to physically cut the revised footage back into the original negatives or master print. It was very damaged by '97 but even the parts that were still in ok shape had to be in fragile condition. Lucasfilm surely couldn't be that stupid to use a patched master print to make all the copies for theatres and then home video. Anyone with 1/4 a brain would use the negatives only when absolutely necessary because the more times they were scanned and run through a projector, there would be a bigger risk that they would crack, or get misaligned and jam. The original negatives and other surviving elements were used used to create a new master print that was the basis for all subsequent copies. Whether they bothered to scan and restore the original negatives of the parts that were completely replaced is unknown. So they for sure had to restore a scene where the only thing changed was a cg ship was added in the background. But wouldn't they have had to restore everything. Lucasfilm couldn't have known to the exact frame which parts were going to be altered.