You may have floorplanned the design and saved it. Then you realize that you must make a change to the design at the schematic level that deletes some logic. When you read in the FNF file, the Floorplanner reads in the old hierarchy. Due to the changes made at the schematic level, the old hierarchy may represent divisions that are no longer valid.
You must select a hierarchical node to enable the Flatten Groups command.
This procedure explains how to flatten the hierarchy in the Design Hierarchy window.
To rebuild the hierarchy using symbol instance names, select Hierarchy Rebuild. The Floorplanner builds a hierarchy tree and places the selected logic symbols in their proper positions in that tree.
The Rebuild command works on all logic, not just selected logic.