War Commander will periodically save your game progress for you, but if anything interrupts the save function (a hiccup in the connection, for example), it will cause that save to fail.
*Note: If you do not log in for 48 hours, your repairs will stop. This is an intended feature.
This can interfere your offline repairs, upgrades, and builds along with it. If you're encountering these issues, try these steps to improve your chances of repairs continuing even when you are offline.
1. Set whichever platoon you wish to repair
2. Wait for red save icon in top right corner to turn from red back to gray
3. Exit the storage or platoon window
4. Do something else on your base to trigger another save, this can be anything, such as collecting resources or starting an upgrade
5. Wait again for the red save icon to turn gray
6. If you are done, log out. Adjusting your repairs again means you will need to start over with this process.