The folder/file structure in the working copy is either existing fully or not at all (apart from deleted or new objects). However, different parts may be in a different revision depending on the last save or update time of individual objects. When you open a project, the project and the user libraries under version control therein are completely updated from the nested working copy, and then the working copy is in turn refreshed from the resulting project (all existing objects in the project are rewritten, but nothing is deleted from the nested working copy automatically).
The project working copy is initially created completely on activating the checkbox Activate version control for this project under or by a checkout operation from the repository of the project.
The library working copy is initially created completely on activating the checkbox Activate version control for this user library (only possible if project is under version control) from the user library's property dialog or by a checkout operation from the repository of the library.
On save of a changed existing object, this object is re-written into the working copy.
On deletion of an object, this object is deleted from the working copy (manual work necessary on working copy).
On creation of a new object, this object is added to the working copy (manual work necessary on working copy).
On renaming of an object, this object is deleted from and re-added to the working copy under its new name (manual work necessary on working copy).
On close of the project, all objects are re-written into the corresponding working copies.
On switching from online mode to offline mode, all objects are re-written into the working copies.
On open of a (version-controlled) project, the project is emptied and rebuilt from the project working copy and then all objects are re-written into the nested working copy.
Contained user libraries under version control are deleted and re-created from their corresponding library working copy and then their objects are re-written into the corresponding library working copies.
The project working copy is not deleted automatically if a project is deleted.
However, if a user library inside is deinstalled, deleted or taken out of version control by deactivating the checkbox Activate version control for this user library (only possible if project is under version control) in the library's property dialog, the corresponding working copy will be deleted from inside the project working copy. You may receive a message asking for confirmation.
If an old working copy is blocking the creation of a new working copy or if it is outdated, you may be asked to confirm its deletion. If you do not confirm, the current action may have to be cancelled.