Metrics, Visualization and Data model got disappared after dataset refeshed.

I am using PowerBI service to build a report.

That is very risky.  Anyone can create a PBIX with the same name, upload it to the workspace and destroy your work.  There is no Undo or Redo button in the service.   I know Microsoft is working on feature parity between Desktop and Service but we are still far away from that. 

At a minimum make regular backups by downloading the PBIX.