Due to limited and faulty communications, company commanders and orderly sergeants who kept company rolls clearly did not know what had happened to anyone not actually in camp. Put yourself in their position - how would you know what had happened to Private Jones who was left sick along the road or sent to a medical facility? Hospitals moved frequently, and hospital records went with the hospital staff. For that matter, hospital clerical staff had the same communication problems as orderly sergeants. A hospital director was required to complete rolls and forward them to the Medical Director's office. However I don't know of a regulation that required communication with a patient's unit commander.

Based on what I know of company records, orderly sergeants often recorded word of mouth information and best guesses about men away from camp.

Let me suggest that you read one of the recent publications about Confederate hospitals. If you understand Confederate medical records, how they were kept and for what purpose, it should help.

http://books.google.com/books?id=wCZMNDkMbNAC&dq=isbn:0865549710
http://muse.jhu.edu/login?auth=0&type=summary&url=/journals/bulletin_of_the_history_of_medicine/v082/82.1brieger.html

http://www.sc.edu/uscpress/books/1996/3155.html
http://www.lib.utexas.edu/taro/utcah/00042/cah-00042.html