at the moment phpBB has only one root folder.
Please make a separated root folder for all data uploaded by users and for other things like database backups.What's the problem?
Then you are updating or modifying phpBB then your are uploading data.
Then you are backing up your forum then your are downloading the files.
To be sure and to prevent corrupted data successfully you have to remind to the folders which are containing the file data. If you are stressed or if you are a newbee then you don't forget to unselect these folders.
Also there is a risc with dangerous FTP client settings: http://blog.phpbb.com/2011/08/23/the-da ... #more-5341
So if you are uploading destroyed backuped data then your data - e.g. images and uploads - is lost.
Then you are moving to a new server then you can have problems, too.