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.
I made over a Large Backpack with 10 Items inside and none of the items inside were made over. Fortuneatly, I had renamed the Pack so I was able to go one at a time to make over the 10 items.
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 :)