China DOS Union

If it can be used on the command line, then it can be written into an automatic batch file.
Find and replace, or start at a certain byte position and overwrite 3 bytes, for example: 888
If not, then I'll just write one myself.

Re atoms:
change will do. It can be used on the command line, and its output can be suppressed, though the parameters are a bit troublesome. It used to be available for download in the New DOS Age.
String usage: change filename /form apple /to banana
Decimal usage: change filename /from \010 /to \010\013
Hex usage: change filename /from &h0a /to &h0d&h0a

Also, one called hexc.exe works too, and the parameters are relatively simple. I originally downloaded it from "Qibu":
String usage: hexc oldfile newfile "string1" "string2"
Hex usage: hexc oldfile newfile 0a 0d0a
Mixed usage: hexc oldfile newfile "apple"0d0a "apple"0d0a" "