Continental collision is not an instantaneous event, but may take several tens of millions of years before the faulting and folding caused by collision stop.
The thinnest continental crust is found in rift zones, where the crust is thinned by detachment faulting and eventually severed, replaced by oceanic crust.
Just what happens in a specific orogen depends upon the strength and rheology of the continental lithosphere, and how these properties change during orogenesis.