We’re aware of this issue: there must be one SonarCloud analysis per GitHub repo, if there are more than per repo, we are not yet able to aggregate them. This is on our radars, but it won’t happen very soon.
The way to go is to run a single SonarCloud analysis for the entire repo. And this is certainly possible, because we do the same in multi-module gradle projects at SonarSource. I suggest to look into the documentation of the Gradle scanner. You may get inspiration from how we did it for the sonarqube project.