A student asked this in class. I was legitimately stumped and am having a hard time finding information. We discussed the pros and cons in class (hard time arguing you're a free country if you keep people from voting, but Southerners might be inclined to vote McClellan to end the war, difficulty of counting votes during war, what this means for the legitimacy of the North and South). It generated really good conversation, so I was hoping you might be able to help shed some light!
The 1864 election was only held in Union states. So if you lived in an area/state that had been in the Confederacy, you would not have had the chance to vote - even if your city had since fallen under Union control.