[{_id:1,name:"Joe",myAreas:[{_id:"1a",isActive:false,myOtherId:"1a1",area:"Gaming"},{_id:"2a",isActive:false,myOtherId:"1a2",area:"Fishing"},{_id:"3a",isActive:false,myOtherId:"1a3",area:"Cooking"},]},{_id:2,name:"Joe",myAreas:[{_id:"1a",isActive:false,myOtherId:"1a1",area:"Gaming"},{_id:"2a",isActive:false,myOtherId:"1a2",area:"Fishing"},{_id:"3a",isActive:false,myOtherId:"1a3",area:"Cooking"},]}]

db.collection.update({},{$set:{"myAreas.$[x].isActive":"TRUE","myAreas.$[y].isActive":"FALSE",}},{arrayFilters:[{"x.myOtherId":{$not:{$in:["1a1","1a2"]}}},{"y.myOtherId":{$in:["1a1","1a2"]}}],multi:true})