Some cells might have been eliminated from the current design, or moved during placement, leaving orphaned route segments from the reference design. If you are running in the Vivado IDE, you might see potentially problematic nets. These orphaned or improperly connected route segments are cleaned up during incremental routing by the Vivado router.
The following INFO message appears during placement.
INFO: [Place 46-2] During incremental compilation, routing data from the original checkpoint is applied during place_design. As a result, dangling route segments and route conflicts may appear in the post place_design implementation due to changes between the original and incremental netlists. These routes can be ignored as they will be subsequently resolved by route_design. This issue will be cleaned up automatically in place_design in a future software release.