Hi Marina
I decided to check the upgrade doing it the way you described: upgrading the same site instead of creating a new site. I ran 2 tests, and I have conflicting results.
The first test:
- Installed a fresh copy of Moodle 3.1
- Imported from our site 3 courses which have orphaned sections. The import was successful, the sections stayed orphaned.
- Switched branch (git) and got latest version of 3.3 from Moodle on Github
- Installed (via FTP or CLI) a couple of course formats and themes that the courses needed.
- Went to the site and did the upgrade process successfully
- The sections became hidden and their activities are available to students. Success!
The second test:
- On our current site (3.1)
- I switched branch (git) and got latest version of 3.3 from Moodle on Github
- Installed (via FTP or CLI) all formats, themes, question types, etc. and assorted plugins that the courses needed.
- Went to the site and did the upgrade process successfully
- The sections stayed visible. Failure.
Since the process of getting the 3.3 version was the same in both tests, and the change was in the plugins installed (in the first test only about 5 plugins were installed, but in the second test we installed dozens of plugins), I'm thinking that some plugin was at fault. I don't know which plugin, and the process of elimination would be too tedious, but just updating this info here, in case someone has an insight on the issue.