Hello Stephen,
Could it be that the two paths resolve to different directories? Could you open project properties and then expand Resource->Linked Resources category and look at "Path Variable" tab. It should show all linker resource paths, you should be able to see actual resolved paths there. If they point to the same physical direcotry, (ABC and ABC1), then is there any way that you could provide a bit more detail in how linked resource paths were created? A sample projects would be ideal, but I am not sure if it is possible.
I tried importing couple of projects from ControlSuite SW package, which use linked resources quite heavily and copying couple of linked files from one project to another did not create duplicate linked resource path variables.
martin