This happens because of locked resources while upgrading. We recommend to stop all BizTalk360 runtime resources before upgrade so no reboot is requested. To stop BizTalk360 runtime resources do the following:

  • Stop BizTalk360 monitoring service
  • Stop the application pool called BizTalk360 in IIS

If it still prompts for a reboot, it could be because of a pending reboot because of some other software upgrade/install.