My understanding on this is incredibly limited and you may want to wait to hear back from a modder who knows more of what they're talking about.
That being said, when I have manually installed FX mods, they have gone under the new data file you have to manually create in your games folder.
Perhaps do a backup of that data file (in case you have to roll back) then delete the corresponding FX file associated with bio armour.
Other idea is to troll through the COH modder thread and see if there is anything there on uninstalling mods.
