There are 2 synchronizations possible : directories/files and file metadata. directories/files is about synchronizing your directories tree with the category tree in the database. metadata is about updating elements informations such as filesize, dimensions in pixels, EXIF or IPTC informations.
The first synchronization must be the directories/files one.
Synchronization process may take long (depending on your server load and quantity of elements to manage) so it is possible to progress by step: category by category.