Just considering how a lot of other political unions got started; I can think of Hawaii as a notable region that got annexed. Considering how so many of them are large and plentiful enough to be thriving countries in their own right, were any others given ultimatums, outright annexed, etc?
Well, since you say "complete"...western Virginia was, for the most part, not wanting to secede with the rest of Virginia in 1860. When it did go through the process of having the constitutional conventions necessary for the region to become a separate state, some counties ( mostly the eastern panhandle) were not particularly interested in leaving Virginia but were thought necessary by the rest to have in the new state because of things like railroad connections. While most counties were asked to send delegations to the conventions, for these few counties , if they did not send a delegation to say otherwise, they were counted as voting yes. These were under control of the Union Army at the time, and of course there would have been no way to have a free election for any delegates , let alone some who might vote no.
Not the most scrupulous process, perhaps, but I am sure that some Civil War historians could also comment on states like Missouri and Tennessee that had significantly big regions that did not want to secede from the Union but , since they were never allowed a plebiscite on the subject found themselves in the Confederacy regardless.