Hi Luca
I've moved this discussion to the developers forum while we get things sorted out.
I don't know why it's not working for you. We've just run a test, upgrading a Moodle 4.5 server with serveral courses to Moodle 5.0 and the existing questions work fine. However, we did do the upgrade with the development branch of coderunner in place, which you didn't do, so that might be a factor. All the same, if the prototypes are present in the Front Page question bank, you shouldn't be seeing the errors you're seeing since the new version of the code includes that context in all searches for prototypes.
So, can you clarify what you mean when you say "I can see the PROTOTYPE questions in the right spot I think", please?
On my Moodle 5.0 system, if I click the Home link (taking me to the Front Page course), and then choose the Question banks link, I get told that the "Question banks in this course" are the System shared question bank (a link). When I click that link I see all the CodeRunner built-in prototypes.
Is that working for you?
Richard