In my opinion, deleting files from other developers is not necessarily the way to go.
If you have two AFCADs for the same airport from different developers, you should delete one of them because, even in the unlikely case they were both made perfectly aware of each other, so you won't see any double objects, the sim WILL load them both, which is a waste of resources.
But that's the ideal case: the most common case, is that if you have two AFCADs for the same airport from different developers, they usually cause issues like double objects, AI problems, duplicate navaids, etc, since most of the AFCADs that come with 3rd party airports are designed to work only to replace the default one.
I think you should adapt the software to the environment and not the other way around.
In this case, GSX is helping you finding a conflict that you would have to resolve anyway.