Disconnecting from a project erases the working copies of files on your computer while leaving the master copies on the Version Cue Workspace intact. Disconnecting also removes shortcuts to the project from the Adobe dialog box. You may want to disconnect to free up more space on your hard drive. Or, you might disconnect from a project if someone else in your workgroup deletes a project from the Version Cue Workspace (your working copies are not touched by that deletion).
As long as you have saved a version of the working copies there is no harm in discarding them by disconnecting. When you access the project again, new working copies will be created for the current versions of the files you open. If you have working copies with the In Use By Me status, you will not be permitted to disconnect from a project until you have saved a version of those files.
When you disconnect from a project, only the working copies and shortcuts on your computer are erased. Leaving the project intact on the workspace allows others, as well as yourself, to access the master files. When you delete a project, all working copies and shortcuts on your own computer, along with the master copies of files and folders in the Version Cue Workspace, are erased. However, any working copies and shortcuts on other computers your co-workers or you previously used to access the project are not erased. To completely remove the project and erase those working copies and shortcuts, you must select the shortcut or project folder and disconnect, even though the project has already been deleted.