I wanted to share a batch file that I run every time I do a nightly update. I rename the koreader directory to something like koreader.A and make sure the batch file is in the koreader.A directory. I then put the new koreader directory in place. Running the batch file from the koreader.A directory gets all the current changes. Because I use Ken's uimanager.lua script changes to get it to sleep correctly I always make a backup before overwriting it. Good thing too because last week I had to fix the uimanager.lua.
After the batch file copies dictionaries and history to the new directory it copies itself. You have to be running the batch file as administrator for that part to work.