It is Summer 1481 and my second generation has reached Soverign (though it is now near the end of his life). My problem is that looking at the office listings there is no Emperor - nor has there been for at least 8-10 years....
So there is no way for me to progress into the final part of the political game (I am already grey eminence but was after chancellor)...
Anyone had this happen to them and anyway to fix other than start again and hope the emporers don't die off?

If you got a message that the emperor has died and he hasn't come back yet then as Drlstvaan said it could be a historical part of the game. If however you never had any message about his death it would probably be a bug in the game. There doesn't appear to be a solution for it other then restarting your game.
I would send a ticket off to gog tech support eitherway as they try to look into game bugs and fix them if at all possible.

The odd thing was that an emperor was apparently still giving out titles to my opponents...
Hehe a short while after that my character died at the ripe old age of 50....
One year later the unknown emporer died and a proper one went into place - time to start with the next generation for chancellor!

Glad it got solved for you!
Good luck on your new political career!