Yes, but he hasn't agreed to that. I was telling him he could weasle his way out of dealing with your war at great cost to himself 

And this is 1700. You know how much brainwashing was done back then, how effective it was etc? Yeah, good luck. Not to mention, if your lands are vast and made up of many peoples, you are forgetting that most probably aren't Germanic. The Empire trait isn't just positive, it carries negatives. You are made up of many peoples, not just Germans and Slavs. Also, are all your soldiers going to like shooting each other, their families and friends and countrymen? 
And Numburg is running on an entirely different political system. I cant imagine many people in Numburg, their navy, army or people suddenly being fine with an emperor and an entirely new system. Also, given that corporations rule numburg, many of them wont want any risk to their power. In other words, expect an uprising of powerful and rich companies. Likewise, I cant imagine the Lance royalists would be fine with dropping the Emperor just for unity, and even trying to reach a compromise between the two would be incredibly hard and obviously there would still be resistance. You still haven't addressed your loyalists. Lance loyalists would still be a problem, by this I am referring to your nationalists and the sorts. They will, even if they believe in the deal, like their nation to be disproportionately in charge, meaning they will want the other under their thumb and their own flag to be flown over the others lands instead of a new flag.
Then you will have inevitable resistance. Obviously you cant have two competing command structures, two competing institutions etc, so people will likely end up laid off, reassigned or merged with others, resulting in discontent in your own government. The supreme leader of both armies wouldn't like the idea of the other replacing him..

Tl:dr
There will be violence, every unification in history that I can recall has involved, the exception being the Anschluss, but those were two down trodden, small countries and not two successful, large countries (And certainly neither was an Empire any longer) Yours will just be on a massive scale because rather than the usual scenario with two small countries joining, you're two massive countries, one of which already has many countries within jt.