Problems like this occur when packets of data are lost or mixed up in transit between your system and our servers. In this situation, your final commands -- the ones setting your repairs -- aren't making it to our server. This results in what is called a "Failed Base Save".
There are a couple of steps you can take to more securely lock in your progress and save your base before closing the game.
- Bank all of your resources from one of your generators.
- Launch a fleet to the World Map
- Switch to the World Map view and recall the same fleet
- Return to your Base View
- Close your game
If you've taken these steps and you're still experiencing lost time on your repairs, let us know and we'll be happy to help out.