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Do you have "Automatically create prospects in Pardot if they are created as a Lead or Contact in Salesforce" enabled on your SFDC to Pardot connector? If not, this option will make sure any contacts/leads in SFDC with an email address are synced to Pardot so Pardot can match the prospects you are importing on the Pardot side.
If your database is under 50K, you could also try to trigger a full sync by creating a new custom field and just deleting this field when you are done. More info here: https://help.salesforce.com/articleView?id=pardot_prospect_full_sync_options.htm&type=5