[{"_id":"3981396a-9fcb-4c24-976f-d500f20c4fab","entries":[{"key":"var1","value":"value1"},{"key":"var1","value":"value11"},{"key":"var2","value":"value2"}]}]

db.collection.update({},[{$set:{entries:{"$reduce":{"input":"$entries","initialValue":[],"in":{"$cond":{"if":{"$in":["$$this.key","$$value.key"]},"then":"$$value","else":{"$concatArrays":["$$value",["$$this"]]}}}}}}}],{multi:true})