First of all, to make sure that the relevant teams notice your post, it’s good to optimize the tags on your post. I suggest to add jacoco, gradle and coverage tags. I suggest to remove sonarcloud and sonarqube tags when posting in the Get help / SonarClod category.
If I understand correctly, you managed to merge the coverage report of all modules into a single report file, and the analysis result on SonarCloud shows coverage only for the main app, and not for any of the other modules. If this is not correct, please clarify.
The first thing I would check is look inside the report file and make sure it really contains what you expect.
Then I would check the scanner output, if there are warnings related to importing the coverage report. A common problem for example is that the report file references file paths that don’t exist, The scanner output (./gradlew sonarqube ... --info) would show warnings for those.
I noticed that the official guide for importing jacoco coverage report mentions a link to handle multi-module projects that might also be helpful.