Well, firstly this is a beta so expect lots of updates to the game over the next couple months with the intent to provide feedback on the latest version.

Regardless, you should familiarize yourself with how to turn off automatic updates if you choose to play long games over a period of time and don't want your save file impacted.

We can't guarantee compatibility, but you may be able to work around this issue by doing the following:

1. go to 'C:\Users\yourusername\AppData\Local\Ironclad Games\Sins of a Solar Empire\Save-SinglePlayer' 
2. change the file extension of any '.save' file to '.savereb'
3. restart Rebellion
4. You should see them in the list of saves, but no guarantees they will load properly

Great. I just forced myself to stop playing just to be greeted by the update message