The small program that I'm attaching causes the topological iterator of GstBin to think that a loop has been detected while there isn't one.

The topological iterator not only depends on the presence/absence of the children, but also on their linking. So the cookie its uses should be invalidated on links. I'm afraid we'll have to listen to the GstPad::linked/unlinked signals in gstelement and then have gstelement emit a signal/message that gstbin can catch to update the cookie...