Axis & Allies Developer and Playtester; War of the Ring Editor and Playtester
There are four cards (from a quick scan) that have this prerequisite in bold at the top of the card, my question is that these cards do not affect the Fellowship if the region (with the settlement) is under shadow control i.e. it is still a Free People's settlement irrespective of control.
I see it that way because I note that the FAQ has a few specific clarifications adding the bolded condition 'controlled by the Free Peoples' to the rules in question, thus inferring that those rules without that phrase do not require control by the Free Peoples.
Control of the Settlement doesn't matter.
And while I'm here the 'Foul Thing from the Deep' card in this set states you must eliminate a companion (if there are any) to reduce damage (if any) - I'm assuming that you may use options 1 & 2 ('cards on the table' and 'guide sacrifice') on p41 to first reduce the damage so long as the final act, before taking any remaining damage as corruption, is the random companion sacrifice ?
You may reduce the Hunt Damage using play on the table cards and Guide special abilities (not elimination) before taking a random casualty.