This is due to white-listing, one way to handle that is just ensure the include and exclude lists are always identical between 'base' and 'updates'.

In CI we have an extra layer of point-in-time mirrors we can use to actually isolate upstream repo changes from the system, but we didn't implement the code to consider changes to these repos as separate change streams yet. This, of course will only become useful once we prevent the VMs from bypassing this and going directly to the upstream repos.