I'm not sure what would happen in FTL's case, but all the experience I had with other games is that all the data of progress, etc. should not be missing after updating.
Just to be safe - backup your iPad, then update the game, If the save/progress data is missing, restore the device form backup. After restoration iOS will automatically install the game version which has been backed up, so there will be the old version of FTL with your data intact.
(Note - that retroing form iCloud backup may take some time depending on you internet speed. If fast it may take 5 to 10 minutes. But if slow... it may as well take 3+ hours).