I think I noticed this problem to. In my only campaign I've played so far (it brutally ended when my Windows collapsed a week ago
). It was 1380something when the HRE lost their capital, they didn't die out because of it (they were filthy rich) but they did rapidly shrank and, strangely, they never attempted to recapture it (I'm pretty sure cause I kept an army of agents all over central and western Europe). And, also, by the year 1420 (the year my XP collapsed), too many a faction had disappeared (Hungary; Venice; Angevin/if that's their name; Denmark; Armenia; Timurids; Fatamids; Altan... and France) but I haven't asked myself why 'cause one of those early deaths (Hungary) was caused by me
so I thought others must be a result of warfare too. Well, I know for sure that Denmark and France was terminated by England who exploded and whipped them both out one at the time. As for the others, I haven't payed attention but given the German case it could be the loss of Capital that triggered it.
So, I'll download the recommended fix as soon as I reinstall the game and see what happens in my next campaign...