Interesting - I made over a city and used the 'Make over contents' tick box, and it worked fine. It doesn't list the things that are made over as well, but in the event it does say X number of [entities] made over as well.
Gideon, I used it for the large pack I bought off you recently and it worked. This was a few weeks ago though, so it likely just got messed up with some new update. Hopefully it'll get fixed soon as it's pretty handy, especially for you I can imagine :)