Upgrading Notes version 9.0.1FP7 to Notes Version 11.0.1 causes Notes preferences settings to reset in default settings after the upgrade. Users need a way to conserve these settings so they don't need to setup/configure their Notes preferences settings again and again after each client upgrade.
Most of the preferences are stored in the workspace folder where eclipse components are being stored. The way some of the workbench preferences were saved has changed with the eclipse platform upgrade. Due to the eclipse upgrade, the current preferences set by the users will be lost. As of the moment, there is no way to preserve these preferences since after the eclipse upgrade, it is needed to launch Notes Client with the -clean switch to clean the configuration. This is working as designed.