phpbb_is_writable() method of the filesystem class truncates files when trying to check for wtitability here:
The cause is that fopen call parameter was changed from 'r+' to 'w'. The latter causes truncating files, see http://php.net/manual/en/function.fopen.php
'w' Open for writing only; place the file pointer at the beginning of the file and truncate the file to zero length. If the file does not exist, attempt to create it.
This can lead to f.e. truncating config.php when entering ACP main page.