reference manager is made for this kind of thing.
No, it is not (as far a I know):
Standalone reference manager application does not allow changing attachment to overlay status. Unfortunatelly.
Reference manager as internal command allows it only one by one clicking per file . That is no multiple selection, no batch processing, no nested file treatment etc.
Furthermore command-line version does not include subcommand for changing the status, thus it is unusable for this topic completely.
Or am I missing something?