[{"subs":[{"name":"subrepo1","files":[{"name":".....","spec":"Unknown"},{"name":".....","spec":"Unknown"}]},{"name":"subrepo2","files":[{"name":"file2","spec":"Unknown"},{"name":".....","spec":"1234"}]}]}]

db.collection.aggregate([{$unwind:"$subs"},{$project:{"subs.name":"$subs.name","subs.files":{$filter:{input:"$subs.files",as:"file",cond:{$eq:["$$file.spec","Unknown"]}}}}},{$group:{_id:"$_id",subs:{$push:"$subs"}}}])