Chiming in with my experiences --
Definitely agree with @brian_mullins and making sure LTIs and subaccount admins are checked.
I work at a large K12 with about 184 subaccounts (and their courses) that need to move into parents based on their school's grade levels (high, middle, elementary) and had to do this after our rollover in the summer.
Two things to take note:
1) If you do have another system that impacts account structures, like a SIS -- make sure that "process as UI changes" is enabled so that your work isn't undone. (Ask me how I know. 😆)
2) Through the UI you can only do one SIS import at a time. If you use the API you can "load" other SIS imports (this is how I could do an account re-structure then blueprint courses)
I always suggest the following with SIS imports:
1) Test in your beta instance first to see if the structure is correct!
2) Do SIS imports during a downtime to minimize any impact.
Hope this helps!