When you get this warning you should just select 'yes to all'. This warning often occurs on files that are actually the same, they just have different dates on them. The 'yes to all' option is the recommended way to deal with the warning.
As for deleting the cache file this will not remove the extensions. The extensions will only be removed if you delete the entire configuration folder. Sorry for any confusion on that as the instructions are both on that page. You should try deleting the WinFileCache or MacFileCache depending on your OS.