There is an issue with the eShop this morning for those who are trying to get the updated Mighty Switch Force.  WayForward says not to delete/redownload the game if you already have it:

Deleting and redownloading MSF will result in a loss of data, and you’ll end up with the old version again. Hold tight, we’re working on it!

Update: Looks like the new update is now working—-If you are trying to update, just go to the Settings/Other section in the eShop, then ‘Your Downloads’.