There are many different reasons why a saved report would be missing but a less obvious cause is when a perspective that has dependent reports is deleted.
Saved reports that are dependent on perspectives will be removed if the perspective is removed. We warn of this when archiving a perspective. For example, here is a simple saved report, named 'Test Report With Perspective', that uses the 'Demo Practice' perspective:
If I now go and archive 'Demo Practice' perspective, a popup will appear stating that dependent reports will be deleted:
Here is what is presented when attempting an archive of the 'AssetGroup' perspective:
We provide a similar confirmation screen when attempting to delete a group within a perspective. Any reports dependent on that group will be deleted.
Re-naming a perspective, or a perspective group will not delete reports.