When you reset a contact and you do not tick the box to delete their previous answers, then the links between the contacts and their previous answers are broken. The previous answers of the contacts remain in the survey and are available in the reporting and downloads.
This means that you won’t be able to filter directly on contact metadata. Say you have placed the employee department in custom field 1, what you need to do is create a hidden drop-down question to hold that information and pre-fill it with the custom field 1. That way, you will be able to filter on ‘department’ in the reports.
This is an important article to read on the subject:
Capture contact data in hidden questions