I'm not sure if this is exactly what you're asking, but you can reset coverage metrics in the org by opening Developer Console and using
Test | Clear Test Data. Unfortunately there's no public API for that, so I've not been able to integrate it into Illuminated Cloud directly.
You can also remove the IDE's cached test by going into Illuminated Cloud | Manage Coverage Reports, selecting the coverage report for the org, and clicking the '-' button in the toolbar.
Between the two, that should reset the coverage information on both sides.
Please let me know if that doesn't help and/or wasn't what you were asking.
Regards,
Scott Wells