[{"_id":1,"tagsGroup":[{"id":"1234","tags":{"m1":1,"m2":2}},{"id":"456","tags":{"m3":1,"m2":2}},{"id":"1234","tags":{"m4":2,"m5":2}}]}]

db.collection.update({"tagsGroup.tags.m2":{$exists:true}},[{$set:{tagsGroup:{$map:{input:"$tagsGroup",in:{$mergeObjects:["$$this",{tags:{$arrayToObject:{$map:{input:{$objectToArray:"$$this.tags"},in:{k:{$replaceOne:{input:"$$this.k",find:"m2",replacement:"m6"}},v:"$$this.v"}}}}}]}}}}}],{multi:true})