how to use $elemMatch with $in operator in the match section of an update command....for reference check out the below command:
Db.collection.update({participants:{$elemMatch:{participant:{$in :[1,4,5]}}}}, {$set:{"participants.$.removed": true}})
Below is the document:
{
"_id" : ObjectId("590c24e76c8e0669334b68a5"),
"name" : "The Group Name 2",
"participants" : [

{ "participant" : 1, "admin" : true, "deleted_at" : null, "added_after" : null, "exited" : false, "removed" : false }

,

{ "participant" : 4, "admin" : false, "deleted_at" : null, "added_after" : null, "exited" : false, "removed" : false }

,

{ "participant" : 8, "admin" : false, "deleted_at" : null, "added_after" : null, "exited" : false, "removed" : false }

,

{ "participant" : 5, "admin" : false, "deleted_at" : null, "added_after" : null, "exited" : false, "removed" : false }

]