By default it does already - see
Modify > Expert > Copy/Delete > Advanced > 'Make safe copies...'
precisely for that reason.
But it absolutely does not delete Destination files 'en masse' and then start copying file #1 (#2, etc) unless you specifically tell it to via
Modify > Expert > Copy/Delete > Advanced > 'Delete ALL files on...'
which for obvious reasons is off by default. Moreover, it would delete every file in the Destination (if a single-Zip, in the Zip), not just the ones to be replaced. The deletion happens before the scan, so it wouldn't yet know which the latter were anyway, and after the deletion of all files, it wouldn't matter anyway ('nothing to scan' = 'copy all')
What it sounds like to me is that your source disk (before it died altogether) declared lots of files as not present on the Source (because it was faulty), and your profile is (presumably?) set to delete files from Destination if not (apparently) on Source - so it did.
Modify > Expert > Copy/Delete > Advanced > 'Make safe copies...'
precisely for that reason.
But it absolutely does not delete Destination files 'en masse' and then start copying file #1 (#2, etc) unless you specifically tell it to via
Modify > Expert > Copy/Delete > Advanced > 'Delete ALL files on...'
which for obvious reasons is off by default. Moreover, it would delete every file in the Destination (if a single-Zip, in the Zip), not just the ones to be replaced. The deletion happens before the scan, so it wouldn't yet know which the latter were anyway, and after the deletion of all files, it wouldn't matter anyway ('nothing to scan' = 'copy all')
What it sounds like to me is that your source disk (before it died altogether) declared lots of files as not present on the Source (because it was faulty), and your profile is (presumably?) set to delete files from Destination if not (apparently) on Source - so it did.