The main point of files synchronization is that files are stored on both local PC and server and changes are applied for both local PC and server. 

Files located on server are changed rarer than database. So system administrator should make changes in both server and local copy. Then local copy with the applied changes should be packed and stored with other backup copies. .

These are the files which are often changed on server:

• file in ../files (for Drupa 5) and ../sites/default/files (for Drupal 6)

Revision Control

It is a good idea to make revision control. For example, list what changes for what files were made in a text file.

You can use any revision control version (CVS, SVN etc.). All these systems allow to log changes.