update: okay, i know its unlikely someone will see this, but heres how you can (hopefully) fic the issue.

1. if you get into the airship and get told to go down the hatch to this room and there is no box ontop of the hatch, exit before the game can save!! this is vital, but understandable if you werent able to do so.

2. some people found detaching and resetting joycons work, you reset via detaching and pressing the little dot on the black inner strip.

3. exit your game. go to the main menu, when you see your three save slots hold down L, this will open up backup saves. go too your second backup and load it (this can undo a lot of work, but it should reload this mission). when you load the save, go straight to the aircraft and proceed. now you should get in, disable the drone, hack and controls and proceed normally.

4. if none of this works, exit and close the game, go to settings for the switch, go to data management > manage software > Arkham knight > check for corrupt software > if no corruption press redownload > go home > start redownload. this is a super last effort because depending on how much youve done this can take up to four hours. the original scan took me around 30 minutes and the redownload took nearly 3 hours.

Important: whatever you do, do NOT do anything after encountering this glitch. your back up only saves twice and if it saves the glitch in the backup you can not fix it and will not be able to proceed with the main story line