I never thought to use the backports repo in Jessie to keep pacemaker installed. That's a great idea, I'll give it a try and see what happens.
Regarding Pacemaker's data and config, as far as I could tell, it was gone. I'm not positive what happened with it, but I wonder if the fact that the pacemaker package was missing entirely from the new release caused apt to just get rid of it during the upgrade. I can also re-try that and keep closer track of what gets removed. I do know that when I upgraded from Wheezy to Jessie and then to Stretch, and then I re-installed Pacemaker in Stretch, it didn't find any old config data and acted like a new installation.