I'm going to go speculate wildly here, so bear with me. Some of the posters claim that they can see unstable locations and vortices on the Innsmouth board. If so, those six Deep One Uprising tokens are probably used in the same way as the Dunwich Horror tokens, except I imagine that when the Deep One Uprising track is filled the Investigators immediately lose the game.

Now, what if the raid on Innsmouth is represented in the game by a Rumor? A rumor which is difficult to pass, perhaps requiring multiple things to be done. If you fail, the Deep One Uprising takes place and you lose. If you succeed, not only are you rewarded with Clue tokens, but you basically kill the Innsmouth board. The Uprising trak will never advance, maybe even no new gates will be able to open on the Innsmouth board for the rest of the game.

Or maybe the raid will be represented by a Mythos card which returns all monsters on the Innsmouth board to the cup, but that seems so much less interesting to me.

It probably be a mechanic independant from a single card, to avoid dilution issues. Compare Kingsport and Dunwich for example.

That would be like ending the game if the DH woke up. I think having too many deep ones would just result in something incredibly tough, like Dagon and/or Hydra stalking the streets (need to fill out track twice for both which adds more screwage) or sealing the area so you can never enter it, giving the possibility of having, say, 4 gates you can't seal w/out hopping into one that goes to the same place. And once there every monster and half fish starts heading for you as you try to escape (a la Dark Corners of the Earth)

I think that a Deep One Uprising track filling up will cause many negative things for the Investigators, but wouldn't result in the loss of the game. Despite all the bells and whistles added in each expansion, the focus is still Arkham. Sure, ignoring the rifts in Kingsport or ignoring monsters in Dunwich will put you on the super-fast-track to loosing, but they don't necessaily mean that the players loose. I don't think that FFG would change this formula in a new expansion.