When you deactivate a form and people are in progress with that application you get a notification "X copies of this Application have been started and saved an applicant. Would you like to allow these in-progress Applications to be submitted?"
You need to hit YES. Then it will deactivate, Applicants who have started the application can finish, and you can make changes and reactivate. 

NOTE that when you make changes only the people who click on the link AFTER the changes are made will see them. ANYONE who has already access the form will NOT see any changes. 

If you want to Force an update to the application then deactivate it. Selecting NO to "allow these in-progress Applications to be submitted". Modifying the deactivation message to let applicants know you had to change the form you and they will need to start the updated application and put the link to the application to do so (you will have to get the link before deactivating the form). Anyone who has already started the application will see the message and then have the link to start the application again (after you reactivate it).