The first step is to make sure you have a backup of the notes/data directory. I recommend CrashPlan+. The family plan is hard to beat in price if you have more than one computer or a couple of VM's. It allows you to do offsite cloud backups, with up to 10 computers, unlimited in size. Additionally, you can backup to a local drive, NAS or friends computer (free, free, free). There's no excuse not to do backups.
With that out of the way, the Working Sets are stored in a file in your notes/data directory:
notes\data\workspace\.metadata\.plugins\org.eclipse.ui.workbench\workingsets.xmlEach time Domino Designer starts up with blank Working Sets, close Notes and Domino Designer, restore the file mentioned above from your backup system and start Notes / Domino Designer.