I've got some save games where I have the issue. Most recent is
this one where I have not been able to revoke titles since my current emperor (previously King of Saxony before inheriting the imperial throne) has not been able to revoke titles since his election, and in many cases has not been able to replace flank commanders. (Sometimes he can replace one flank comander, but after even that flank is greyed out.)
It may have to do with Saxony having a low tribal organization, but that's not something I can check without opening the savegame which I haven't done. I had the issue with previous rulers too, and was able to clear it up, possibly by switching primary title, but I don't think you can switch primary to a kingdom when you're emperor.