there seems to be a fear that "overwriting" one folder with another will overwrite all the files. this is not the case. when you upload a folder to the server when there is already one there with the same name, it does not replace the one there with the new one. It can only overwrite files of the same name. which is what you want to happen. in the case of the images/store and files folders it will overwrite the phpbb files but leave all your images ( in the images folder ), your attachments ( in the files folder ) and your database backups etc. ( in the store folder ) untouched.
this is the standard way that uploading/overwriting etc. has always worked.
now, of course it is always a good idea to backup before just to be safe, but the bottom line is that the only thing you really need to worry about is to not overwrite your existing config.php file with the new blank one that is in the new phpbb files .
I am not suggesting that you not follow the instructions here about saving those folders, just trying to explain why it does what it does etc.
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