It would be technically and legally impossible for any of the former Confederate states to have a government entity within their borders that today wouldn’t be considered part of the Union.

This is due to the manner in which states rejoined the union in Reconstruction. The states took the necessary action (ratifying or adopting constitutional amendments, promulgating new constitutions, etc.) to rejoin the union. This means all their political subdivisions essentially were swooped in with them. A state’s political subdivisions (counties, cities, organized towns, etc.) had fealty to the state, are created and authorized by state law or constitution, etc. While an individual jurisdiction could have opposed rejoining the union, or even voted against ratification of a constitution to facilitate joining the union, it still doesn’t sever them from the state itself.

Now, there were instances like Newton Knight and Jones County, Mississippi where there were rebellions against the Confederacy in the late American Civil War.

And, during the secession period, there are isolated instances of some jurisdictions declaring themselves as the opposite of what their state did. For example, Van Zandt County, Texas, has a lore that at one time it was established as the “Free State of Van Zandt,” because it didn’t vote with Texas to secede from the Union. However, it really didn’t happen like that, and there are in fact multiple possibilities for how the county came to be known as the “Free State of Van Zandt.”

Sources: Manning, Wentworth. Some History of Van Zandt County. Homestead Company, 1919 (reprint available on Portal to TX History)

Kozlowski, Gerald F. “Free State of Van Zandt,” Handbook of Texas

Limon, Elvia. “What’s the meaning behind the ‘Free State of Van Zandt’ motto? Curious Texss Investigates,” Dallas Morning News, Feb. 1, 2019.

“Free State of Van Zandt chronicled,” by Faith Harper, Tyler Morning Telegraph, Oct. 24, 2017