Now you can also use variants of pick (or omit) given a sample.yml file of:

myMap:
  cat: meow
  dog: bark
  thing: hamster
  hamster: squeak

then

yq '.myMap |= pick(["hamster", "cat", "goat"])' sample.yml

will output

myMap:
  hamster: squeak
  cat: meow

See https://mikefarah.gitbook.io/yq/operators/pick#pick-keys-from-map