I see so the best advice would be to clean everything unless boss or the mod author instructs otherwise doing both "remove identical to master records" and undelete and disable references"?

Always undelete and disable, regardless. Otherwise yes, unless specific instructions say not to clean, always remove identical to master records.

There is absolutely NO genuine good reason for a deleted record, unlike some very rare identical to master records where they are genuinely needed.

Ok thanks, i'd better start cleaning