Could you give us more details? How was the ‘versioning’ done, did you give the workflows new names?
Some details about you machine and disk might help.
Then: KNIME basic version does not have a dedicated versioning or auto-save feature, the KNIME server has that.
I once suggested a do-it-yourself backup system but this is more a sorry excuse for a real backup.
In general you should think about a backup system where your work gets saved, stored and versioned (think TimeMachine on Mac or Dropbox or OneDrive).