Analyse, if this problem really affects your instance with:

select course from mdl_course_sections where section = 0 and visible = 0;

This returns a list of all affected course ids. Then you can manually change the visibility of these default sections to 1 with:

update mdl_course_sections set visible = 1 where section = 0 and visible = 0

Afterwards, you either need to purge all caches or you need to make any change to each affected course (such as adding modules, hide unhide module, move modules) so that the course cache is invalidated and rebuild.

Before upgrade:

1. Create/use a course in topics format, hide one of the sections, make sure there is at least one activity in the general section (usually announcements), remember course id
2. Create/use a course in weeks format, hide one of the sections, make sure there is at least one activity in the general section (usually announcements), remember course id
3. Open adminer/phpmyadmin/etc and execute: update mdl_course_sections set visible=0 where section=0 and course in (?,?) where (?,?) are two course ids you noted above
4. Purge all caches
5. View these two courses, make sure that your general section is displayed as hidden and the activity in it "available but not visible"
6. UPGRADE
7. View these two courses, make sure that the general section and activity in it is now visible but the other section that you hid is still hidden