Yeah that is because you are playing on a region, and backing up a region save does not back up all of the sub colonies, you can only do cross-platform region game with cloud sync right now. That is a separate issue though, if you want to test this on 0.78.0 you would have to start a new game for testing purposes.
Anyway, I am going to go ahead and start compiling the bug fix update after lunch here and see if it helps. The issues may be fixed, but I have been unable to test them to verify. If the issues persist, I will hopefully be able to get more feedback and analytics data tracked before v0.79.