When using the incremental mode or analyzing short living branches, files have a status detecting if they were unchanged, added or changed in the current analysis.
If files are unchanged they aren't analyzed by the sensors, and the CE will simply keep the latest copy of those files and their issues.
As a side effect, SonarJava won't analyze directories that contain only unchanged files. The reason is that there is no way of directly getting the directories, so they check the parent directories of the files that they analyze (and they don't analyze unchanged files).
The consequence is that the issues on those directories will be closed and then reopened again as new issues in the next time we do a full analysis.
If we add in the scanner a "unchanged" status to directories containing only unchanged files, the CE will keep the issues on those directories.