Dear Roman,
As also noted in my private E-Mail to Stephen, one issue highlighted here is the lack of notification about such issues with the probe. For instance I didn't notice that anything is wrong until almost a month later (and by then it was already difficult to pinpoint these issues to the configuration changes that I made earlier), as there is no E-Mail notification for probe connection flapping, only for 60+ minutes periods of disconnection. So perhaps it would be a good idea to consider adding more kinds of E-Mail notifications to Atlas in the future.
You can set a pretty aggressive (down to 10 minutes) notification threshold on the probe status page. I do not recommend this in general, since it's going to be way too noisy, but it may come handy if you're testing something. Regards, Robert