You can delete an existing version by selecting it in the Version Manager and pressing the Delete Version button. Note, however, that when you delete a version, you also automatically delete all previous versions.
When you delete a version, the version number is never used again. For example, if you had a single version (1.000), and you deleted this version and then re-enabled versioning and created another major version, it would be numbered as 2.000.
If you choose to delete the most recent version (and hence all versions in the model), GoldSim will automatically disable versioning (until you enable it again by creating a new version).