Strangely, I have exactly the same problem on my MacPro but not on my MacBookPro. I changed the sidebar on both computers to contain my favourites but after closing all the windows on the MacPro or restarting, the sidebar returns to its defaults.
hmmmm... I am also having the problem with a MacPro 5,1 mid-2012 10.12.16
I was also experiencing some full blank screens as I tried to create new browsers from saved settings. So I de-registered and used AppDelete to get rid of any "extra pieces" or legacy files in case they were creating the problem. Then I reinstalled PF8 but unfortunately I experienced the same issues.
At this point I have downgraded to PF7 (7.6.2), seems to be a couple too many issues with this version and I need to get my work done. PF7 works fine for me and the features are good. I also find the sidebar in PF7 to be easier to use than PF8.. not sure why though. And it remembers the favorites which happens to be the primary feature that I do use.
In addition, on my MacPro PathFinder regularly freezes when I try to close a window (spinning ball of death) and I have to force quit it. Never had this before. I might have to go back to v. 7 just as you did.