Database
[{"balances":{"intraday":[[1630939075734,1899.09],[1630939435939,1899.32],[1632306730756,0],[1632306759376,0],[1632272012916,1372.22]]}}]
Query
db.collection.update({},[{$set:{"balances.intraday":{$filter:{input:"$balances.intraday",cond:{$ne:[{$arrayElemAt:["$$this",1]},0]}}}}}])