Rubuta ci gaba ga wannan sakin layi - An sake sanya Cooper a matsayin laftanan-kolonel na 4th Kentucky Cavalry a ranar 26 ga Maris, 1863 kuma ya zama colonel a watan Afrilu; biyo bayan murabus na Col. Bayles. A ranar 4 ga Yuni, 1863, Cooper ya ji rauni lokacin da doki ya fadi a kansa a Franklin, Tennessee. Ya umurci rundunar a yakin Chickamauga a watan Satumba na 1864. Cooper ya koma Lexington, Kentucky a 1864 don izinin rashin lafiya. Daga nan Cooper ya jagoranci sojojin gida a kan 'yan fashi na John Hunt Morgan. Ya ki amincewa da bukatun Morgan don mika wuya na Lexington a ranar 9 ga Yuni, 1864 kuma ya sake dawo da dakarunsa. A watan Afrilu na shekara ta 1865 ya umurci sakon Montgomery, Alabama kuma a watan Mayu da Yuli na shekara ta 1865 a Albany, Georgia. An ba shi izini a ranar 21 ga Agusta, 1865 a Macon, Georgia. Ya sami girmamawa na yaƙi don hidimarsa a Shiloh, Koranti, Richmond, Chickamauga, Morgan's Raid zuwa Kentucky, Yaƙin Resaca da Raid na Wilson akan Montgomery. An ba shi izini ga Lieutenant Colonel da Colonel a cikin Rundunar Sojoji a ranar 2 ga Maris, 1867, don kyawawan ayyuka a yakin Resaca
a Georgia da kuma kama Montgomery, Alabama.