There are two different types of synchronisation:
Synchronising directories and files is about updating your directories tree with the album tree in the database. Synchronising file metadata is about updating photo information, such as filesize, dimensions in pixels, EXIF or IPTC information, in the database.
When synchronising your uploads with your gallery you must first synchronise directories and files.
The synchronisation process may take a long time (depending on server load and the number of elements to manage) so it is possible to do it album by album.