I guess I've found a bug in the way the sonar-scanner-engine handles shutdown SonarQube servers when retrieving project's quality profile.
I am personnally randomly facing the exact same problem and finally managed to reproduce the issue.
How to reproduce :
1) Let P an existing project, with former analyses along with issue statuses saved, and its java profile set as desired-profile
2) Stop SonarQube server
3) Start new analysis using sonar-maven-plugin in debug mode (breakpoint set to org.sonar.batch.repository.DefaultProjectRepositoriesLoader.load(String, boolean))
4) Step return out of load method (you can see here that a brand new org.sonar.batch.repository.ProjectRepositories is returned)
5) Now start SonarQube server
6) Disconnect debug process
The analysis resumes with the default java quality profile set, but not even the slightest hint of alert is logged. At the end of the process, it is being sent to the up-and-running server but the analysis is saved with issues that are not part of the quality profile desired-profile.
Even worse, the statuses of previously managed issues are reset.
In real life, this may occur when SonarQube is under maintenance or is restarting.