There have been several threads recently on cities that just seem to disappear. Here, I'll try to cover some of the reasons, and some of the recovery strategies. This thread applies only to SimCity 4 Deluxe. Further knowledge in this is welcome. This is what I know about it.
Prevention
Never switch away from the game during a save. The game is very sensitive to loss of focus during this process and may fail or corrupt your city. There are at least two bad things that can happen here:
The city appears as a green area in the region view. This is recoverable (usually).
The city is gone and there is a hole in the region view. This needs recovery actions that may not be available to all.
Make sure your game is up to date for published patches. As issued on CD, the game is full of bugs corrected by patches published by Maxis. Your game version needs to be at 1,1,638 to be free of Maxis known problems at the time of the patch issuance. Your version should be at 1,1,640 if you expect to get full use of all the custom content available. The digital download of Deluxe (1,1,641) includes the above mentioned fixes, and runs with no CD in the drive. To access the CD patches start here. You may have to register at SC4Devotion for this.
Recovery
Case 1.1 above. Simply open the city. It should just open. When it does, do an internal save (CTRL+s) to reset the region snapshot.l
Case 1.2 requires some work.
If you have a backup for your region, simply locate the city in the backup and place it in the <you>/documents/SimCity 4/Downloads folder. Now open the game and click on the empty space. When the open city dialogue appears, simply click on the import city icon (left most one) and navigate to the recovered city in the Downloads folder. All done.
You don't have a backup. For this case it depends on whether or not you can render the region again. If you do not have a .SC4M file nor a gray-scale .jpg + config.bmp files, you cannot do this. Pass to the next item.
If you have the files, create a new region folder with a different name and copy the base files to this folder. Switch to the folder in the case of a .SC4M file render the region with SC4Terraformer in the usual way. In the case of gray-scale + config.bmp files, open the game, open the new (substitute) region and render it. Close the game.
At this point you have a complete layout of the cities in the region including the one that is "lost". The trick now is to locate the proper file since they are all pretty anonymous at this point. Open the game and choose the new region. On the "lost" city, click on it to open it and give it the same name as the lost city. Save and Exit the game -- no switching out.
You can now open the new region and find the "lost" city. This is the same as having a backup, so follow the instructions in 2.1 above.
This is the ultimate bad luck case. There is no recovery know to this author, so you can either live with the missing city, or abandon the region. Sorry about that.