Add some functionality to the Autoloader, check in folder, or Check in project that would allow users to delete or remove broken references if the files are legacy or known problems exist (old logos for example) let the tool warn the users that removing the references may damage the dataset but load them into the vault regardless.
this would be really helpful for secondary bulk loads after preliminary scans and loads have been completed, saving time having to manually interact with old potentially useless files, that need vaulted for safe keeping/single source creation.