The SonarLint plugin ignores settings (i.e. deactivated rules) from a non-default Java quality profile for the connected project on the SonarQube server.
Code lines matching the deactivated Java rules are marked as “issues” by the SonarLint plugin. On the SonarQube server these “issues” are correctly absent.
In earlier (but recent) versions of SonarLint (and/or IntelliJ) this seemed to work.
IntelliJ IDEA 2019.2.1 (Ultimate Edition)
Build #IU-192.6262.58, built on August 20, 2019
SonarLint IntelliJ 126.96.36.19912
SonarCube server: 188.8.131.5201