Database
[{_id:"609bcd3160653e022a6d0fd8",companies:{apple:[{product_id:"609bcd3160653e022a6d0fd7"},{product_id:"609bcd3160653e022a6d0fd6"}],microsoft:[{product_id:"609bcd3160653e022a6d0fd5"},{product_id:"609bcd3160653e022a6d0fd4"}]}}]
Query
db.collection.update({},[{$set:{companies:{$arrayToObject:{$map:{input:{$objectToArray:"$companies"},in:{k:"$$this.k",v:{$filter:{input:"$$this.v",cond:{$ne:["$$this.product_id","609bcd3160653e022a6d0fd4"]}}}}}}}}}],{multi:true})