With that amount of missing data, it is unlikely that Duplicati can recreate the files. Can you post the log data for a repair run?
No. Duplicati will not continue if remote data is missing, as this would create partial backups that are unlikely to be restoreable. Can you pick one of the reported missing filenames and look at the NAS for clues about where it went? Is it still in the folder? Is it a limit on the number of files listed (FTP can sometimes truncate the list)?