Using PathfindingProject_Pro_WebsiteDownload_4_2_4_75066e20.zip
Repro:
New project
Import PathfindingProject_Pro_WebsiteDownload.unitypackage
Add component Pathfinder
Add Layered Grid Graph
Click scan: Red boxes show up as expected
Select a different object in the Hierarchy OR move the mouse over the transform widget.
Bug: Red boxes disappear
Hi
I cannot replicate this in an empty scene. Which version of Unity are you using? Can you replicate it in an empty scene?
It’s a new project. Version 2018.2.18f1.
From that screenshot, if I press Scan again the red boxes show up until they disappear again
Also been seeing the same for a while. Currently on unity beta2018.3.0b6.
My reproduction:
Created new project, added A* pro 4.2.4, loaded Example10 (Layered recast example).
Toggled ‘Show Unwalkable Areas’ on in Settings-> debug,
Scan - Unwalkable red cubes show at boundaries/unwalkable areas until next scene view update (mouse move over scene view - they disappear)
Same also happens for the regular grid graph.
Certain editor interactions will show them again temporarily (Inspector updates, tooltips appearing).
Edit: Looks like the DrawUnwalkableNodes section might not get cached, so RetainedGizmos.DrawExisting doesn’t re-draw them when the graph’s not been updated that frame.
Hmm… I will check this in a newer Unity version, I have only tested it in Unity 5.2.2 so far (lowest version that this package supports), it might be something that Unity has changed in a newer version.
It is a known issue that the unwalkable nodes will not be drawn whenever any graph updates are being done or the graph is being scanned, but it does not seem like that would be the case here, so the DrawExisting method would not be called.
Possibly some change has been done in Unity which makes the renderedFrameCount not update in the scene view any longer, that could break things.
Hi
I managed to replicate the issue with a newer version of Unity and I have found a fix for it. It will be included in the next update. Thank you for reporting this! 
