People have been trying to explain this to you for the last seven pages.
Odyssey settlements do not follow the pre-odyssey rules for changing ownership in a war.
They have a different, independent set of rules to determine who controls them when the dust settles.
Whoever completes the most zones
at that settlement controls the settlement at the end of the war.
The
sole exception is if the losing faction has
no other assets whatsoever and an odyssey settlement is chosen as their "defend" objective in the right hand panel, in which case the winner will take whichever settlement is specified.
It is possible to take several, or all of the settlements in a system in a single war.
In one particularly busy long weekend, I claimed
sixty settlements in one war by fighting a single engagement at every settlement in the system. Three of those settlements remained in the losing side's hands because other people showed up and did zones for the defenders at those settlements.
None of the stuff you're describing in the old worlds is remotely unusual. I'm actually surprised it took so long in an area that gets that much player traffic.