I did some experiments with this. On rye I have to admit. Rye in general has lower falling numbers than wheat (i.e. rye has higher alpha-amylase activity).
The one result: The starter still works fine, but not as good as with normal non heated flour.
I guess this is because of the enzymes killed in the flour and with just the enzymes produced by the micro organisms the starter doesn't have that much food.
Also I had the sensation, that the starter got sour more quickly. But this could be the same phenomenon: Less food -> earlier overproofing.