What is version of the 3.1 ... highest?
'correct format' meaning the stock (part of core) 'topics' course format? How about in the 3.1. ... is that the highest 3.1? Does it have any non-stock course formats (an addon)?
In the 2.7.20, take one of these problem courses backup it up, then restore it to the 2.7.20 - not same course, but new course in a hidden category and as hidden course. Does it restore with same format?
In the restored copy of the course, change the course format from 'topics' to 'weekly' check it, .... does it exhibit any un-desired results in format? Then reset to 'topics' again.
Have you tried making a no user backup, selecting only one of the resources in section 1 and then skipping down to one of the other sections and selecting only 1 resource there in the backup. Restore that small course to the 3.1 ... what happens?
Shouldn't have to do all this, but ....
'spirit of sharing', Ken