db={"vulns":[{"_id":1,"advisoryId":"44444"},{"_id":2,"advisoryId":"55555"},{"_id":3,"advisoryId":"66666"}],"tracker":[{"_id":1,"customerId":"12345","advisory":{advisoryId:"44444"}},{"_id":2,"customerId":"12345","advisory":{advisoryId:"55555"}},{"_id":3,"customerId":"12456","advisory":{advisoryId:"55555"}}]}

db.vulns.aggregate([{$lookup:{from:"tracker",let:{advId:"$advisoryId",/** put the customerId here*/custId:"12345"},pipeline:[{$match:{$expr:{$and:[{$eq:["$customerId","$$custId"]},{$eq:["$advisory.advisoryId","$$advId"]}]}}}],as:"found_trackers"}},{$match:{"found_trackers":[]}},{$unset:"found_trackers"}])