When you delete a report, any report views created from that report are also deleted. This is intentionally done to avoid "orphaned" report views (views that cannot run because their base report no longer is accessible).
The most likely reason that saving changes to an existing report would delete the associated views for that report is if you use the Save As option instead of using the Save option.
The Save option updates the existing report and retains associated report views.
The Save As option, even if you use the original name of the existing report, deletes the existing report and creates a new report with a new ID. As part of the process of deleting the existing report, all report views are deleted as well.