Efficient way to update contacts after data validation

Hi all, 

We recently used a 3rd party for data validation. I now have a CSV file with contacts that are still valid, and a seperate CSV file for contacts that are no longer valid. The latter set is the set I'd like to deactivate/delete/remove them from our database. Is there an efficient way to do this in bulk, without significant risk?

Thanks in advance for any suggestions.