I have been using "Replace all" for all of the recent updates and have not had any problems. I used to go through manually and found that the files in question were just support images and things that were not really different but had a different creation date.
Make sure that DW is not running, uninstall the extension first (saves a lot of time), say yes to overwriting all, and be patient while Extension Manager does it's thing.
I could never understand why Adobe didn't include a "Overwrite all older files" option.