If you recently updated to version 1.86 and your save game no longer works you can use ConvertData_Rebellion.exe to fix your save game.
1. Copy your save game (likely located somewhere like C:\YourName\Documents\My Games\Ironclad Games\Sins of a Solar Empire Rebellion\Save-SinglePlayer) to your Sins Rebellion install (likely c:\Steam\steamapps\common\Sins of a Solar Empire Rebellion).
2. Open the command window here. (start->cmd, cd\steam\steamapps\common\sins of a solar empire rebellion).
3. Type "ConvertData_Rebellion saveGame yourSaveGame yourNewSaveGame" in the command window.
4. Copy the new save game back to the location from which your save game originally was found.
5. Restart Sins and load the newly fixed save game.