Enlisted men could not resign. I have never heard that any great number of enlisted men deserted to join the Confederacy and I'd like to see a source for that. If so they should have suffered the fate of the treasonous rats of the St Patrick's Battalion.

The 6th Cav (originally 3rd) was authorized as a 12 company regiment in 1861. It served as a regiment from at least 1862 until it suffered devastating losses in men captured at Fairfield, PA at the time of the Battle of Gettysburg on. Individual companies of the 6th continued to serve until the end of the war.

Volunteer cavalry regiments if recruited to full strenght followed the 12 company organization authorized for the 6th Cav, and 2 compamies were added to the 1st through 5th Cavalry Regiments in the summer of 1862.