A user is a person who logs into Runn and can access data. They may also be listed as a resource and have work assignments for your projects on Runn. Though they are the same person and connected via their email address- they act like 2 separate entities in Runn.
Deleting a user will simply remove their permissions and they will no longer be allowed to log in and access your Runn dashboard or timesheets but the data added for their resource profile will remain.