I don't think that checkbox will be the answer for this issue in my experience. I think what you should do is download an SIS export report from your root account, selecting the users CSV option, then filter down to your 50 students you're trying to suspend and change the status column there, then re-upload. When I have run into this error in the past, it's been caused by the login being restricted to a certain provider in either Canvas or the CSV file (but not matching). For the info to update, things need to match perfectly, otherwise Canvas will thing you're trying to create a new user/login, but be unable to as the sis_id is already in use. By starting with the sis export report file, you'll be guaranteed to have all of the fields populated correctly.
Hope this makes a bit of sense and helps you out!
-Chris