@LindsayDew Welcome! You're doing what I would do in the case of deleting the courses using the SIS export for the SIS-created courses and then modifying the column. I will caution that Beta/Test will operate slower than the live production version of Canvas. Beta/Test do not like overly large files to be sent through the SIS system, they often will get stuck and require intervention through the API to cancel the job.
What I usually do with bulk actions and testing is to dump around 100 - 200 lines into a new file and send that file over to Beta/Test -- if there's an issue usually it gets caught within that file. I would try that in beta/test if you're not having success with a SIS import.
For the non-SIS courses I haven't found a good way to deal with that. I usually end up using an API call to modify these courses (often times they're courses manually created by our subaccount admins). Maybe someone else will have a better idea on how to manage those courses.
