First of all, please check if the downgraded enemy Brotherhood Bastion matched the level, specified in the upgrade requirements. These requirements can be found in the Brotherhood Bastion window.
Also, please, make sure that when the battle at a rival Brotherhood Bastion took place, your own Bastion was on the appropriate level.
Like in every other quest or event, it is necessary to have the upgrade requirements present on the list, to be able to fulfill them.
Whenever your Brotherhood Bastion level changes, the old requirements disappear, since they are substituted with the new ones. If the downgrade requirement was not fulfilled, then it is most likely that you did not have it in your Bastion, when the battle took place.
In other words, when you downgrade an enemy Brotherhood Bastion to fulfill the level 9 upgrade requirements, your own Bastion should necessarily be on level 8 at the time of the time of the downgrade.
Nevertheless, you only need to complete Bastion downgrade requirement once on each level. Therefore, if your Bastion was downgraded, you will not have to downgrade a rival Brotherhood Bastion again to bring your own Bastion back to it's previous level.