"Uncontrolled" refers to the Powerplay power in control, not the Minor Faction. It is irrelevant to either superpower or minor faction rep.
Your reputation with a minor faction does not decay. If you were Allied with that faction, then you should still be Allied with that faction, uless you subsequently went around blowing their ships up.
Two things may explain your observations:
- The minor faction owner of the station may have changed. So you are still Allied with the minor faction, they no longer control the station nor have any say in whether you are Neutral, Friendly etc in the space controlled by the station.
- If the faction is aligned with a superpower, then perhaps you were actually Allied only with the superpower, and not with the minor faction. Prior to 2.0, if you were Allied with a superpower, you became instant Allies with every single faction aligned with that superpower. It was a powerful effect - too powerful, because 2.0 local faction rep changed. Now, if you want to be Allied with a minor faction, you have to actually do jobs for that faction. The only advantage being Allied with a superpower brings now, is that it takes fewer missions to become allied with an aligned faction, compared to a non-aligned one.
