I've finally found a way to resrore your lost maps!
1. To get started go to the folder User Data => Backups. There will be a back up, sorted by dates. Look for the time the files supposedly changed.
2. Copy these files somewhere safe.
3. Create in the game a new map. Add a pair of objects to map was not empty. Save, for example, under the name of "new"
4. Then go to the User Data folder and iterate through all the files and folders and look for the one that was created or modified only just . Usually there will be up to 9 files.
5. The copied files in step 2, put with replacement to the folder that you found.
6. Open the config.txt. Find the line "username". There will be quoted in the title of your map that you have lost. change its name to that you gave to the new map. In our case it is "new".
7. Go to the game and enjoy!))
Hope it will help you.
I've already written to support team, so maybe they can do a fix or something like that
