If you set the profile to delete files on Destination that are not on Source, and your system fails to list the damaged files (so it looks as though they are not present) then yes, it will delete the files on Destination (as instructed). It's not psychic.
You can set a max-percent level of deletions in any one run, but we have no way of telling legitimate deletions from 'failed-to-list'. You can use Versioning to keep just [1] Version of anything it deletes with a time-limit to safe-keep copies thereof for [as long as you set] but note that this will also keep [1] 'previous-state' Version of files you edit, too. This is not negotiable.
You can set a max-percent level of deletions in any one run, but we have no way of telling legitimate deletions from 'failed-to-list'. You can use Versioning to keep just [1] Version of anything it deletes with a time-limit to safe-keep copies thereof for [as long as you set] but note that this will also keep [1] 'previous-state' Version of files you edit, too. This is not negotiable.