islandmaan so far you only mentioned the toolbar display change, and the reason for that is pretty clear since it is a widespread phenomenon. That is no “penalty”. You didn’t mention any ranking drop, or especially any significant ranking drop.
The whole phenomenon has been playing out over several months, so there is no way of knowing what will happen next. But if your rankings are the same, don’t worry about it. If for some reason you need to see green in the tolbar on you main page, change you linking so all your tracking links go to site.com/a/?scsr23 Once everything gets recrawled you wouldn’t have the problem you do. Your main page would be unique and your pile of duplicates would all be in a subdirectory you don’t care about ranking for or care what the PR is. Just make the subdirectory page somewhat different than you main page, which you could do easily.