When ywSynch synchs your project it keeps a note of the structure of the project. If you subsequently carry out actions in yWriter like moving, renaming or deleting scenes and chapters ywSynch will detect this the next time it opens the project and will offer to rename and delete remote files to match the new structure. Under normal circumstances, it is highly recommended that you accept its offer to do this.
This means, for example, that if you want to make a yWriter project available to a proofreader you could synch it to a shared dropbox and, as long as you don't both edit the same scenes, the proofreader could modify scenes and you could move them around in yWriter, and the next time you use ywSynch it would be able to synch the proofreader's changes back once it has renamed the remote files.
If you make a lot of changes to the project in yWriter, or you have finished with the remote version of the project you can delete the remote version of the project by selecting Project/Delete Remote. After deleting all of the remote chapter folders and scene files ywSynch will re-display the project in its new state, where all the scenes are At Project Only, and will default to copying them all to Remote when you click Synch.
If you modify anything in yWriter, or change something about the remote project by hand, while a project is loaded in ywSynch you can reload its state by selecting File/Refresh from the menu.
One of the useful features of yWriter is that it allows you to write a synopsis (description) of each chapter and scene, or other notes about it in its Description window, as well as information about characters, items etc. ywSynch automatically copies these descriptions, and places them in the Remote project folder either as html files or pdf files.
The Project notes, Locations and Characters are placed in the remote root folder for the project as separate files. The synposes of the chapters and each scene are placed as one file in each chapter folder.
Note that LibreOffice needs to be installed on the PC to create pdf files. If it is not, only html files can be produced.