Kookoo replace is a command line tool for Windows. Kookoo replace will crawl all the dirs down where it's executed, will find all the files named as it's first execution parameter, including those in archives and will replace them with an "ideal" version of a file that lies alongside the kookooreplace.exe.
kookooreplace file-to-replace.txt jar
Running this in a particular folder will replace all the file-to-replace.txt's in subdirectories. Requires the "ideal" file-to-replace.txt to be in the same directory as executable.