Hi GuyM458,
You have to read things carefully, like many people mentioned this whole post is dedicated to unpairing an Apple Remote and not concerning a universal remote like your Harmony, it seems no-one answering here has a Harmony Remote and we are all volunteering to help each other in our spare time so that's more of a friendly gesture than a right to troubleshooting for you.
There are two different suggestions to fix the Apple Remote unpairing issue on these pages of which I think mine really does unpair it properly (I happened to find out how by trial and error) and the other method seems just a work around to me. My post was clearly a reply to the OP and not to your request.
From reading your posts it seems that you have been mixing both suggestions even though it does not concern a universal remote.
Now a few suggestions that may help you;
How to pair your Harmony remote with just the ATV4 I don't know as I don't own one, this is something you will have to use the Harmony remote instructions/forum for or make a new specific post yourself, also if the work around method you have applied has disabled infrared detection of the ATV4 you will have to find a way to turn it back on again (maybe reversing the steps or possibly returning the ATV4 back to factory settings?).
If the Apple Remote is still working with both your ATV3 and ATV4 then I am sure you can unpair it from just the ATV4 by using my solution (where my Mac Mini becomes your ATV3), just make sure that only the ATV4 is on before unpairing by removing the power cord from the ATV3 first so it does not change any ATV3 settings/pairings.
Good luck!
Danny