Thankfully no, but Deck refreshing is relatively new and likely not had a lot of real world use. I have successfully used it many times for simple deck property updates but to my limited recollection moving decks around can be a bit fraught.
Adding decks to new maps, I am not sure that even needs the refresher - but either way, new decks will be empty in existing scenarios (just like At-Start-Stacks would be). You’d need to do something to populate them with your cards.
@g1ul10 has been asking similar questions recently about new deck issues, guess you’ve seen my replies there and they haven’t helped ?