Yes, you should be able to change the sub-account for a course without any issue from a Canvas perspective.  I recently reworked our sub-account framework and moved whole sub-accounts worth of courses without a problem.

If you want to gain confidence in the process, I  recommend that you take the action in your Test or Beta environment first, and then masquerade as teacher and/or student (if you have that permission) in the course to see if anything is impacted. 

If the course happens to be using an LTI Tool that is only applied to the original sub-account, then that might be one possible impact to check/consider.