This info probably came from the NPS Civil War Soldiers and Sailors System online, and they took their regimental info from Crute's books, which were very poorly researched.
The 12-month soldiers who did not want to re-enlist at the end of their service period, were NOT transferred to the 9th Ky. Inf. At the end of its 12 month service, the regiment was re-organized, and remained the 5th Ky. Inf. This unit did eventually join the Orphan Brigade (in the fall of 1863), but the Orphan Brigade was NOT the Louisville Legion (the L.L. was a nickname for the 5th Ky. Inf., USA).
This regiment did NOT fight at Shiloh or Baton Rouge. That was the 9th Ky. Inf., which was originally also called the 5th (but it wasn't this Eastern Ky. 5th).
While it was broadly included in Gen. Johnston's surrender of April 26, 1865, the regiment did not actually surrender its arms and accept parole until May 6, 1865.
Hope this clarifies some things.
Geoff Walden
5th Infantry Regiment, assembled during the late summer of 1861, included Freeman's Kentucky Infantry Battalion. Its members were raised in the counties of Pendleton, Breathitt, Morgan, Magoffin, Bath, Owen, Grant, Jessamine, Henderson, Harrison, Shelby, and Franklin. Being a twelve-month unit, when it became time to reenlist some of its members refused and were transferred to the 9th Kentucky Regiment. Later men of the 5th did reenlist for the duration of the war. It became part of the Orphan Brigade or Louisville Legion. The regiment reported 134 casualties in the Battle of Shiloh, then was active at Baton Rouge before being assigned to Kelly's and J.H. Lewis' Brigade, Army of Tennessee. It was prominent at Chickamauga and later took an active part in the Atlanta Campaign. In the fall of 1864 it was mounted, aided in the defense at Savannah, and fought in the Carolinas. The unit had 91 men disabled at Chickamauga, totalled 201 men and 165 arms in December, 1863, and surrendered on April 26, 1865. Its field officers were Colonels Hiram Hawkins, Andrew J. May, and John S. Williams; Lieutenant Colonels John W. Caldwell and George W. Conner' and Majors Richard Hawes and William Mynheir.