Deleting a user in Vidispine does not delete it completely, instead it the user is disabled and thus unable to to sign in anymore. A disabled user can later be enabled again. To disable a user you call the API with DELETE, like this DELETE /user/(username) (see Disable user in the API documentation). You can later re-enable the user using a PUT to the API PUT /user/(username)/enable (see Re-enable user in the API documentation). You have the have administrator privileges to be able to disable or enable a user.
This is ok most of the time, but sometimes you need the user to be deleted completely. For this we have developed a tool that will delete it directly from your database. You can download the UserTool from the Software Downloads/Tools and things section in this knowledge base.
The tool is run with java -jar UserTool.jar and should be self-explanatory. Just make sure the you make a backup before you start, and then you need to reindex of ACL, items, collections. You can read about re-indexing the metadata in the API documentation.