GUIDs should be unique.
One potentially related issue is that the UUID version isn’t specified by buildingSMART, resulting in less random GUIDs. I’ve previously reported this problem here and here.
I am surprised at the frequency and the specificity to the IfcProject entity, though. That suggests it may be a different issue.
I took a look at that IFC file and sorted the GUIDs ascending - there are no internal collisions, and I do not see clearly wrong ones (e.g. sequential GUIDs) within that file. My new theory for this scenario is that perhaps ArchiCAD is generating GUIDs correctly, but perhaps if you load a particular template which includes a project GUID, ArchiCAD will preserve it in subsequent exports? I’m not convinced, though, that 250 files are using the same template …