Alpha acids will continue to isomerize until the wort reaches 79C (175F). Any hops added above that temperature will add bitterness. FO hops will add bitterness, and in my experience, whirlpool hops will still add a little bit of bitterness. However you also get a lot of hop flavor out of those whirlpool additions.
You don't need to remove any hops from the wort when you are cooling. Ideally you should be able to drop to 79C fairly quickly and any added IBU's will be negligible. If it takes you a really long time to get the wort down to whirlpool temps you should keep that in mind when designing your recipe as you'll get a bit more bitterness than planned.