Well, I apped for a card and cloc on the same day and was approved for both - but I did not already have credit with them.
My guess is it is fine to do so - the only thing that may prevent an approval is if you've reached your internal credit limit with NFCU after getting the Flagship. Internal limits are temporary and increase with time.
If you don't mind possibly wasting a hard pull, it won't hurt to try.