RE: Flash player does not work; can not be able.
I've been playing with chrome://site-engagement more. Setting a site to 0, pressing enter and refreshing that page does indeed remove the site from the list.
Also, setting a site to 100 (and pressing ENTER to apply it) and refreshing the site's page often allows flash to work without even adding an exception to the list. I say "often" as it doesn't work all the time. Sometimes I have to close out of the tab for the site and open it up again. Other times I have to repeat that stuff a lot of times or refresh the site page a bunch of times. Then it works, again without adding an exception.
So, maybe try going to chrome://site-engagement and setting all the sites to 100 (making sure to press ENTER each time). Then, for sites where that still doesn't help, keep reloading the site for a while just to see if you can get it to work.
If a site isn't in the list, go to the site first and then it'll show up. If it still doesn't though, you'll have to try the exceptions list. Then it should show up in the site-engagement list where you can then set it to 100.
Not a solution. Just something to mess around with. Also, once it works for a page, I'm not sure if it keeps working (after a restart for example) yet. But, it looks like it persists.