Hi Russel, I tried that last night and I'm getting the same behavior. After performing the steps I re-favorited all the cookies and DBs that I wanted, and I still get the odd click/unclick when trying to favorite a flash cookie in Chrome.
I'm using 5.5.8 on OS X 10.11.6, Chrome 61.0.3163.100. I use the advanced UI mode, and I can not favorite any Flash cookie - if I click the checkbox it immediately unselects. As a result when I exit Chrome all flash cookies are cleared, including ones I want to keep.