Below steps should be followed to assure a problemless non-problem upgrade to the latest version of TFS4JIRA Self-Hosted.
Please open IIS manager (command: inetmgr) and STOP application pool named: TFS4JIRA Sync App Pool
In order to be 100% safe please backup the database file with the current configuration.
the configuration file is by default present in this folder: C:\inetpub\wwwroot\tfs-jira-synchronizer\App_Data (please look in other/custom location if you performed custom TFS4JIRA installation)
database file name: config.sdf
please copy this file to a safe location, for example, your desktop