Hello!
I have this odd issue where when my project is opened through ‘Load Latest Project’ it seems to source some things differently than when opening the project directly by double clicking the .uproject or using the Browse… in project selector.
In UE 5.2.1 it wasn’t anything critical but you could see that Editor settings were different between the two ways of opening a project:
Folder colors were different etc, SaveGames were now sourced from the AppData\Local\UnrealEngine\5.2\Saved\SaveGames folder instead of usual Project Folder, Editor Preferences were changed
Now after upgrading to 5.3.2 it has become an actual problem. When I try to Load Latest Project, it will prompt me with the ‘Cannot Build from Source’ listing every module in my solution. Pressing Yes gives me the failed to build message.
My Binaries etc are fine in the project directory. If I open my solution I can build it just fine. If I open my uproject directly, it opens and works just fine.
It is probably important that my Project Directory is located on the Desktop and thus outside the usual Documents/Unreal Projects/ folder.
Does anyone know anything about whether or not the, ´Load Latest Project´ vs Opening .uproject directly, flows are different or what is going on here? 
Any info at all would be much appreciated!