If do not know but you probably can do it in a single $addField but it would be easier to do it in different stages.
The first $addField will filter out customer_orders with active:true like you do now.
Then a second $addField will $map customer_orders applying the $filter on the inner items.
Use at your own risk:
top_filter = { "$addFields" : {
"value.customer_orders": { "$filter" : {
input: "$value.customer_orders",
as: "customer_order",
cond: { $eq: ["$$customer_order.active", true] }
} }
} }
inner_filter = { $addFields : {
"value.customer_orders" : { $map : {
input: "$value.customer_orders",
as: "customer_order",
in: { $mergeObjects : [
"$$customer_order" ,
{ "items" : { "$filter" : {
input: "$$customer_order.items",
as: "item",
cond: { $eq: ["$$item.active", true] }
} } }
] }
} }
} }