Potentially also a bug report, but I lost my Hegemony commission due to a smuggling investigation that I ignored. However, all factions that were hostile are still hostile, even after the armistice between the Hegemony and them. As well, once I picked up the commission again, and another armistice against the same faction was signed, it brought my rep to -10, even though I was at -75 when I signed the commission (implying that it held the maximum .
I would think that once you are kicked out of the faction, it would act like you made peace with the other faction, or at least after the Hegemony signs an armistice that you should still have your relations repaired.