Database
[{"_id":1,},{"_id":2,"applicationIds":ObjectId("6118491a406fa2002f2d3d3a")},{"_id":3,"configurationIds":ObjectId("6118491a406fa2002f2d3d3b")},{"_id":4,"applicationIds":ObjectId("6118491a406fa2002f2d3d3a"),"configurationIds":ObjectId("6118491a406fa2002f2d3d3b")}]
Query
db.collection.aggregate([{$project:{_id:1,applicationIds:{$cond:{if:{$ne:[{$type:"$applicationIds"},"missing"]},then:{type:"linux",refId:"$applicationIds"},else:"$$REMOVE"}},configurationIds:{$cond:{if:{$ne:[{$type:"$configurationIds"},"missing"]},then:{"type":"linux","refId":"$configurationIds"},else:"$$REMOVE"}}}}])