If you want to modify more than a single element, you simply need multiple arrayFilters, one for each element you want to modify. If I understand your situation correctly you may try the following untested code to see if it works.
uid_1 = 1000
count_1 = 777
uid_2 = 2000
count_2 = 888
db.nonames.updateOne(
{ "_id" : 1 } ,
{ "$set" : {
"skills.$[one].count" : count_1 ,
"skills.$[two].count" : count_2
} } ,
{ "arrayFilters" : [
{ "one.uid" : uid_1 } ,
{ "two.uid" : uid_2 }
] }
) ;
While at it, could you please provide followup and potential mark as solve your thread