It took a while for the war to end. I found two Confederate deaths in Perry County, Missouri after your last battles in the Archibald Hager Diary:

Hager Diary – June 1, 1865 – Charley Pratte was killed by Captain Minor’s Company.
The Perryville Weekly Union - June 9, 1865
CHARLES PRATTE SHOT
This individual who was arrested Wednesday morning of last week and lodged in the Perry County Jail, hath breathed his last. On Thursday evening of last week, he was taken from the jail with orders to convey him to Bollinger County. He was escorted by a squad of Captian Minor's company. He ceased to live on the same night he left Perryviile, and his body now lays beneath the sod.

Hager Diary – February 5, 1866 – One of the 2nd Missouri shot Joseph Pratte, Bernard Pratte’s son. Wound said to be fatal.
Hager Diary – February 8, 1866 – Joseph Pratte died.