Hi Monika,
Unfortunately, unless your courses are setup as blueprint courses, you would not be able to perform a "batch-update" for this sort of issue. The course template function essentially states that when a new course is created in that account/sub-account, it should auto-import that course template into the new course, and it doesn't have any further checks after that is done.
Depending on if work has been done in those courses, you may be able to delete and recreate them, or depending on the number of affected courses, you may need to manually update them or let the teacher's know how to correct the issue by removing the homepage from that unpublished module. If you're savvy with API, there may be some form of API call you can run that goes through each of those courses automatically and removes the homepage from that template module, but this may be more work than it's worth.
A lot of what the best option is depends on how many courses your institution handles, and how easy it is to locate those affected courses and update them.