When p2 repository finished building I update .eclipseproduct and plugin.properties in branding plugin. Since md5 were already generated I run p2.process.artifacts to update md5 sums. However, the branding plugin's qualifier does not change and thus this bundle is not updated and as a result plugin.properties and .eclipseproduct changes that were made earlier don't make it into update. When I view Help -> About I see build number from the previous build.
Do I need to regenerate qualifier for branding plugin after I updated the files, and if yes then how? Or am I doing something wrong that prevents branding plugin from being updated?
Whenever anything changes in a plugin, you must rebuild it (and thus reversion it). p2 uses the ID + Version as the unique identifier for all artifacts.
If you change your branding plugin, you need to rebuild it (using whatever build technology you're using, such as Tycho, PDE/Build, etc...).