Hello @aurelie,
Thank you for your answer.
We are using Maven as a build tool
In Github Enterprise server (2.20.9) , the “Checks” tab in the Pull Requests now shows a screen where it says “Waiting for checks informations” which seems to run infinitely.
But that is because there is an extra setting now at the project level which didn’t exist before. We can see it by comparing these two documentations:
https://docs.sonarqube.org/7.7/instance-administration/github-application/
https://docs.sonarqube.org/latest/analysis/pr-decoration/
And the setting to add is:
This is the tedious part as we have to put this for every project.
I didn’t see the API before, thank you. So i guess something can be done with this : POST api/alm_settings/set_github_binding
Although that would have been nice to keep the same behaviour when there is only one ALM provider configured or at least provide clear instructions to process this automatically after migration.
In the meantime, we kindly asked the people working on the projects to do this by hand so it would take less time. They started doing it, but their silence meant they weren’t very happy for this 
I’ll try to work on a solution for the rest of the projects that weren’t yet setup properly by using the API.
Thank you for your help.
Antony