Minecraft – Reversing Time Set Command

You could try downloading McEdit (I reccomend a 1.3.x version as the 1.4.x versions have been crashing a lot for me) and opening the level.dat of the backup. Then, switch to chunk view with tab, and use right click to drag the world around, looking for anything irregular that might be your city. If you look at all the generated chunks and don't see anything, then you probably made a mistake during the backup process, or a mistake in putting it back, in which case I suggest ensuring that the world name in properties exactly matches the backup name.

Determine the exact chunks loaded by the second area. The chunk numbers show up on the debugging screen by pressing F3. These chunks correspond to MCA files in the region folder of your save. Copy the MCA files in a permanent location, and, once a week, copy over the current files with your backup, temporarily shutting down the server. A batch file can be used to automate this process, if you'd like.

The MCA files hold groups of 32x32 chunks, for a total block area of 512 x 512. For instance, r.0.0.mca holds chunks 0-32 in both x and z directions (and all of y), and so goes from (0,0) to (511,511).